Changeset 11597 for NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex

Timestamp:

2019-09-25T20:20:19+02:00 (5 years ago)

Author:

nicolasmartin

Message:

Continuation of coding rules application
Recovery of some sections deleted by the previous commit

File:

• NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex (modified) (50 diffs)

NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex

@@ -9 +9 @@
 \vfill
 \begin{figure}[b]
+%% =================================================================================================
 \subsubsection*{Changes record}
 \begin{tabular}{l||l|m{0.65\linewidth}}
@@ -20 +21 @@
 \end{figure}
 
+%% =================================================================================================
 \section{Model output}
 \label{sec:DIA_io_old}
@@ -45 +47 @@
 %\gmcomment{                    % start of gmcomment
 
+%% =================================================================================================
 \section{Standard model output (IOM)}
 \label{sec:DIA_iom}
@@ -103 +106 @@
 even without a parallel-enabled NetCDF4 library, simply by employing only one dedicated I/O server.
 
+%% =================================================================================================
 \subsection{XIOS: Reading and writing restart file}
 
@@ -142 +146 @@
 An older versions of XIOS do not support reading functionality. It's recommended to use at least XIOS2@1451.
 
+%% =================================================================================================
 \subsection{XIOS: XML Inputs-Outputs Server}
 
+%% =================================================================================================
 \subsubsection{Attached or detached mode?}
 
@@ -178 +184 @@
 The following subsection provides a typical example but the syntax will vary in different MPP environments.
 
+%% =================================================================================================
 \subsubsection{Number of cpu used by XIOS in detached mode}
 
@@ -192 +199 @@
 \cmd|mpirun -np 62 ./nemo.exe : -np 2 ./xios_server.exe|
 
+%% =================================================================================================
 \subsubsection{Control of XIOS: the context in iodef.xml}
 
@@ -237 +245 @@
 \end{table}
 
+%% =================================================================================================
 \subsection{Practical issues}
 
+%% =================================================================================================
 \subsubsection{Installation}
 
@@ -247 +257 @@
 {Extract and install XIOS} guide provides an example illustration of how this can be achieved.
 
+%% =================================================================================================
 \subsubsection{Add your own outputs}
 
@@ -303 +314 @@
 \end{enumerate}
 
+%% =================================================================================================
 \subsection{XML fundamentals}
 
+%% =================================================================================================
 \subsubsection{ XML basic rules}
 
@@ -314 +327 @@
 See \href{http://www.xmlnews.org/docs/xml-basics.html}{here} for more details.
 
+%% =================================================================================================
 \subsubsection{Structure of the XML file used in \NEMO}
 
@@ -419 +433 @@
 \end{table}
 
+%% =================================================================================================
 \subsubsection{Nesting XML files}
 
@@ -435 +450 @@
 \end{xmllines}
 
+%% =================================================================================================
 \subsubsection{Use of inheritance}
 
@@ -475 +491 @@
 Inherit (and overwrite, if needed) the attributes of a tag you are refering to.
 
+%% =================================================================================================
 \subsubsection{Use of groups}
 
@@ -516 +533 @@
 \end{xmllines}
 
+%% =================================================================================================
 \subsection{Detailed functionalities}
 
@@ -521 +539 @@
 the new functionalities offered by the XML interface of XIOS.
 
+%% =================================================================================================
 \subsubsection{Define horizontal subdomains}
 
@@ -562 +581 @@
 We are therefore advising to use the ''one\_file'' type in this case.
 
+%% =================================================================================================
 \subsubsection{Define vertical zooms}
 
@@ -585 +605 @@
 \end{xmllines}
 
+%% =================================================================================================
 \subsubsection{Control of the output file names}
 
@@ -657 +678 @@
 \noindent will give the following file name radical: \ifile{myfile\_ORCA2\_19891231\_freq1d}
 
+%% =================================================================================================
 \subsubsection{Other controls of the XML attributes from \NEMO}
 
@@ -710 +732 @@
 \end{table}
 
+%% =================================================================================================
 \subsubsection{Advanced use of XIOS functionalities}
 
+%% =================================================================================================
 \subsection{XML reference tables}
 \label{subsec:DIA_IOM_xmlref}
@@ -858 +882 @@
 field\_ref="sst" means that attributes not explicitely defined, are inherited from sst field.
 
+%% =================================================================================================
 \subsubsection{Tag list per family}
 
@@ -1051 +1076 @@
 \end{table}
 
+%% =================================================================================================
 \subsubsection{Attributes list per family}
 
@@ -1286 +1312 @@
 \end{table}
 
+%% =================================================================================================
 \subsection{CF metadata standard compliance}
 
@@ -1298 +1325 @@
 This must be set to true if these metadata are to be included in the output files.
 
+%% =================================================================================================
 \section[NetCDF4 support (\texttt{\textbf{key\_netcdf4}})]{NetCDF4 support (\protect\key{netcdf4})}
 \label{sec:DIA_nc4}
@@ -1315 +1343 @@
 setting the \np{ln_nc4zip}{ln\_nc4zip} logical to false in the \nam{nc4}{nc4} namelist:
 
-%------------------------------------------namnc4----------------------------------------------------
 
 \begin{listing}
@@ -1322 +1349 @@
   \label{lst:namnc4}
 \end{listing}
-%-------------------------------------------------------------------------------------------------------------
 
 If \key{netcdf4} has not been defined, these namelist parameters are not read.
@@ -1367 +1393 @@
 each processing region.
 
-%------------------------------------------TABLE----------------------------------------------------
 \begin{table}
   \centering
@@ -1403 +1428 @@
   \label{tab:DIA_NC4}
 \end{table}
-%----------------------------------------------------------------------------------------------------
 
 When \key{iomput} is activated with \key{netcdf4} chunking and compression parameters for fields produced via
@@ -1414 +1438 @@
 the invidual processing regions and different chunking choices may be desired.
 
+%% =================================================================================================
 \section[Tracer/Dynamics trends (\forcode{&namtrd})]{Tracer/Dynamics trends (\protect\nam{trd}{trd})}
 \label{sec:DIA_trd}
 
-%------------------------------------------namtrd----------------------------------------------------
 
 \begin{listing}
@@ -1424 +1448 @@
   \label{lst:namtrd}
 \end{listing}
-%-------------------------------------------------------------------------------------------------------------
 
 Each trend of the dynamics and/or temperature and salinity time evolution equations can be send to
@@ -1462 +1485 @@
 and none of the options have been tested with variable volume (\ie\ \np[=.true.]{ln_linssh}{ln\_linssh}).
 
+%% =================================================================================================
 \section[FLO: On-Line Floats trajectories (\texttt{\textbf{key\_floats}})]{FLO: On-Line Floats trajectories (\protect\key{floats})}
 \label{sec:DIA_FLO}
-%--------------------------------------------namflo-------------------------------------------------------
 
 \begin{listing}
@@ -1471 +1494 @@
   \label{lst:namflo}
 \end{listing}
-%--------------------------------------------------------------------------------------------------------------
 
 The on-line computation of floats advected either by the three dimensional velocity field or constraint to
@@ -1481 +1503 @@
 are consistent with the numeric of the code, so that the trajectories never intercept the bathymetry.
 
+%% =================================================================================================
 \subsubsection{Input data: initial coordinates}
 
@@ -1538 +1561 @@
 \np{jpnflnewflo}{jpnflnewflo} can be added in the initialization file.
 
+%% =================================================================================================
 \subsubsection{Output data}
 
@@ -1564 +1588 @@
 \end{xmllines}
 
+%% =================================================================================================
 \section[Harmonic analysis of tidal constituents (\texttt{\textbf{key\_diaharm}})]{Harmonic analysis of tidal constituents (\protect\key{diaharm})}
 \label{sec:DIA_diag_harm}
 
-%------------------------------------------nam_diaharm----------------------------------------------------
 %
 \begin{listing}
@@ -1574 +1598 @@
   \label{lst:nam_diaharm}
 \end{listing}
-%----------------------------------------------------------------------------------------------------------
 
 A module is available to compute the amplitude and phase of tidal waves.
@@ -1612 +1635 @@
 We obtain in output $C_{j}$ and $S_{j}$ for each tidal wave.
 
+%% =================================================================================================
 \section[Transports across sections (\texttt{\textbf{key\_diadct}})]{Transports across sections (\protect\key{diadct})}
 \label{sec:DIA_diag_dct}
 
-%------------------------------------------nam_diadct----------------------------------------------------
 
 \begin{listing}
@@ -1622 +1645 @@
   \label{lst:nam_diadct}
 \end{listing}
-%-------------------------------------------------------------------------------------------------------------
 
 A module is available to compute the transport of volume, heat and salt through sections.
@@ -1646 +1668 @@
 \np{nn_debug}{nn\_debug} : debugging of the section
 
+%% =================================================================================================
 \subsubsection{Creating a binary file containing the pathway of each section}
 
@@ -1717 +1740 @@
  }
 
+%% =================================================================================================
 \subsubsection{To read the output files}
 
@@ -1755 +1779 @@
 \end{table}
 
+%% =================================================================================================
 \section{Diagnosing the steric effect in sea surface height}
 \label{sec:DIA_steric}
@@ -1931 +1956 @@
 Both steric and thermosteric sea level are computed in \mdl{diaar5}.
 
+%% =================================================================================================
 \section{Other diagnostics}
 \label{sec:DIA_diag_others}
@@ -1937 +1963 @@
 The available ready-to-add diagnostics modules can be found in directory DIA.
 
+%% =================================================================================================
 \subsection[Depth of various quantities (\textit{diahth.F90})]{Depth of various quantities (\protect\mdl{diahth})}
 
@@ -1969 +1996 @@
 %       CMIP specific diagnostics
 % -----------------------------------------------------------
+%% =================================================================================================
 \subsection[CMIP specific diagnostics (\textit{diaar5.F90}, \textit{diaptr.F90})]{CMIP specific diagnostics (\protect\mdl{diaar5})}
 
@@ -1987 +2015 @@
 the Indo-Pacific mask been deduced from the sum of the Indian and Pacific mask (\autoref{fig:DIA_mask_subasins}).
 
-%------------------------------------------namptr-----------------------------------------
 
 \begin{listing}
@@ -1994 +2021 @@
   \label{lst:namptr}
 \end{listing}
-%-----------------------------------------------------------------------------------------
 
 % -----------------------------------------------------------
 %       25 hour mean and hourly Surface, Mid and Bed
 % -----------------------------------------------------------
+%% =================================================================================================
 \subsection{25 hour mean output for tidal models}
 
-%------------------------------------------nam_dia25h-------------------------------------
 
 \begin{listing}
@@ -2008 +2034 @@
   \label{lst:nam_dia25h}
 \end{listing}
-%-----------------------------------------------------------------------------------------
 
 A module is available to compute a crudely detided M2 signal by obtaining a 25 hour mean.
@@ -2018 +2043 @@
 %     Top Middle and Bed hourly output
 % -----------------------------------------------------------
+%% =================================================================================================
 \subsection{Top middle and bed hourly output}
 
-%------------------------------------------nam_diatmb-----------------------------------------------------
 
 \begin{listing}
@@ -2027 +2052 @@
   \label{lst:nam_diatmb}
 \end{listing}
-%----------------------------------------------------------------------------------------------------------
 
 A module is available to output the surface (top), mid water and bed diagnostics of a set of standard variables.
@@ -2038 +2062 @@
 %     Courant numbers
 % -----------------------------------------------------------
+%% =================================================================================================
 \subsection{Courant numbers}