Changeset 11831 for NEMO/branches/2019/dev_r11085_ASINTER-05_Brodeau_Advanced_Bulk/doc/latex/NEMO/subfiles/chap_misc.tex

Timestamp:

2019-10-29T18:14:49+01:00 (4 years ago)

Author:

laurent

Message:

Update the branch to r11830 of the trunk!

Location:

NEMO/branches/2019/dev_r11085_ASINTER-05_Brodeau_Advanced_Bulk/doc

Files:

• . (modified) (2 props)
• latex (modified) (1 prop)
• latex/NEMO (modified) (2 props)
• latex/NEMO/subfiles (modified) (1 prop)
• latex/NEMO/subfiles/chap_misc.tex (modified) (14 diffs)

NEMO/branches/2019/dev_r11085_ASINTER-05_Brodeau_Advanced_Bulk/doc/latex/NEMO/subfiles

@@ -1 @@
-*.aux
-*.bbl
-*.blg
-*.dvi
-*.fdb*
-*.fls
-*.idx
+*.ind
 *.ilg
-*.ind
-*.log
-*.maf
-*.mtc*
-*.out
-*.pdf
-*.toc
-_minted-*

@@ -1 @@
-*.aux
-*.bbl
-*.blg
-*.dvi
-*.fdb*
-*.fls
-*.idx
+*.ind
 *.ilg
-*.ind
-*.log
-*.maf
-*.mtc*
-*.out
-*.pdf
-*.toc
-_minted-*

NEMO/branches/2019/dev_r11085_ASINTER-05_Brodeau_Advanced_Bulk/doc/latex/NEMO/subfiles/chap_misc.tex

@@ -2 +2 @@
 
 \begin{document}
-% ================================================================
-% Chapter --- Miscellaneous Topics
-% ================================================================
+
 \chapter{Miscellaneous Topics}
 \label{chap:MISC}
 
-\minitoc
-
-\newpage
-
-% ================================================================
-% Representation of Unresolved Straits
-% ================================================================
+\thispagestyle{plain}
+
+\chaptertoc
+
+\paragraph{Changes record} ~\\
+
+{\footnotesize
+  \begin{tabularx}{\textwidth}{l||X|X}
+    Release & Author(s) & Modifications \\
+    \hline
+    {\em   4.0} & {\em ...} & {\em ...} \\
+    {\em   3.6} & {\em ...} & {\em ...} \\
+    {\em   3.4} & {\em ...} & {\em ...} \\
+    {\em <=3.4} & {\em ...} & {\em ...}
+  \end{tabularx}
+}
+
+\clearpage
+
+%% =================================================================================================
 \section{Representation of unresolved straits}
 \label{sec:MISC_strait}
@@ -27 +38 @@
 balance the net evaporation occurring over the Mediterranean region.
 This problem occurs even in eddy permitting simulations.
-For example, in ORCA 1/4\deg several straits of the Indonesian archipelago (Ombai, Lombok...)
+For example, in ORCA 1/4\deg\ several straits of the Indonesian archipelago (Ombai, Lombok...)
 are much narrow than even a single ocean grid-point.
 
-We describe briefly here the three methods that can be used in \NEMO to handle such improperly resolved straits.
-The first two consist of opening the strait by hand while ensuring that the mass exchanges through
-the strait are not too large by either artificially reducing the surface of the strait grid-cells or,
-locally increasing the lateral friction.
-In the third one, the strait is closed but exchanges of mass, heat and salt across the land are allowed.
-Note that such modifications are so specific to a given configuration that no attempt has been made to
-set them in a generic way.
-However, examples of how they can be set up is given in the ORCA 2\deg and 0.5\deg configurations.
-For example, for details of implementation in ORCA2, search: \texttt{IF( cp\_cfg == "orca" .AND. jp\_cfg == 2 )}
-
-% -------------------------------------------------------------------------------------------------------------
-%       Hand made geometry changes
-% -------------------------------------------------------------------------------------------------------------
+We describe briefly here the two methods that can be used in \NEMO\ to handle such
+improperly resolved straits. The methods consist of opening the strait while ensuring
+that the mass exchanges through the strait are not too large by either artificially
+reducing the cross-sectional area of the strait grid-cells or, locally increasing the
+lateral friction.
+
+%% =================================================================================================
 \subsection{Hand made geometry changes}
 \label{subsec:MISC_strait_hand}
 
-$\bullet$ reduced scale factor in the cross-strait direction to a value in better agreement with
-the true mean width of the strait (\autoref{fig:MISC_strait_hand}).
-This technique is sometime called "partially open face" or "partially closed cells".
-The key issue here is only to reduce the faces of $T$-cell
-(\ie change the value of the horizontal scale factors at $u$- or $v$-point) but not the volume of the $T$-cell.
-Indeed, reducing the volume of strait $T$-cell can easily produce a numerical instability at
-that grid point that would require a reduction of the model time step.
-The changes associated with strait management are done in \mdl{domhgr},
-just after the definition or reading of the horizontal scale factors. 
-
-$\bullet$ increase of the viscous boundary layer thickness by local increase of the fmask value at the coast
-(\autoref{fig:MISC_strait_hand}).
-This is done in \mdl{dommsk} together with the setting of the coastal value of fmask (see  \autoref{sec:LBC_coast}).
-
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+The first method involves reducing the scale factor in the cross-strait direction to a
+value in better agreement with the true mean width of the strait
+(\autoref{fig:MISC_strait_hand}).  This technique is sometime called "partially open face"
+or "partially closed cells".  The key issue here is only to reduce the faces of $T$-cell
+(\ie\ change the value of the horizontal scale factors at $u$- or $v$-point) but not the
+volume of the $T$-cell.  Indeed, reducing the volume of strait $T$-cell can easily produce
+a numerical instability at that grid point which would require a reduction of the model
+time step.  Thus to instigate a local change in the width of a Strait requires two steps:
+
+\begin{itemize}
+
+\item Add \texttt{e1e2u} and \texttt{e1e2v} arrays to the \np{cn_domcfg}{cn\_domcfg} file. These 2D
+arrays should contain the products of the unaltered values of: $\texttt{e1u}*\texttt{e2u}$
+and $\texttt{e1u}*\texttt{e2v}$ respectively. That is the original surface areas of $u$-
+and $v$- cells respectively.  These areas are usually defined by the corresponding product
+within the \NEMO\ code but the presence of \texttt{e1e2u} and \texttt{e1e2v} in the
+\np{cn_domcfg}{cn\_domcfg} file will suppress this calculation and use the supplied fields instead.
+If the model domain is provided by user-supplied code in \mdl{usrdef\_hgr}, then this
+routine should also return \texttt{e1e2u} and \texttt{e1e2v} and set the integer return
+argument \texttt{ie1e2u\_v} to a non-zero value. Values other than 0 for this argument
+will suppress the calculation of the areas.
+
+\item Change values of \texttt{e2u} or \texttt{e1v} (either in the \np{cn_domcfg}{cn\_domcfg} file or
+via code in  \mdl{usrdef\_hgr}), whereever a Strait reduction is required. The choice of
+whether to alter \texttt{e2u} or \texttt{e1v} depends. respectively,  on whether the
+Strait in question is North-South orientated (\eg\ Gibraltar) or East-West orientated (\eg
+Lombok).
+
+\end{itemize}
+
+The second method is to increase the viscous boundary layer thickness by a local increase
+of the fmask value at the coast. This method can also be effective in wider passages.  The
+concept is illustarted in the second part of  \autoref{fig:MISC_strait_hand} and changes
+to specific locations can be coded in \mdl{usrdef\_fmask}. The \forcode{usr_def_fmask}
+routine is always called after \texttt{fmask} has been defined according to the choice of
+lateral boundary condition as discussed in \autoref{sec:LBC_coast}. The default version of
+\mdl{usrdef\_fmask} contains settings specific to ORCA2 and ORCA1 configurations. These are
+meant as examples only; it is up to the user to verify settings and provide alternatives
+for their own configurations. The default \forcode{usr_def_fmask} makes no changes to
+\texttt{fmask} for any other configuration.
+
 \begin{figure}[!tbp]
-  \begin{center}
-    \includegraphics[width=0.80\textwidth]{Fig_Gibraltar}
-    \includegraphics[width=0.80\textwidth]{Fig_Gibraltar2}
-    \caption{
-      \protect\label{fig:MISC_strait_hand}
-      Example of the Gibraltar strait defined in a $1^{\circ} \times 1^{\circ}$ mesh.
-      \textit{Top}: using partially open cells.
-      The meridional scale factor at $v$-point is reduced on both sides of the strait to account for
-      the real width of the strait (about 20 km).
-      Note that the scale factors of the strait $T$-point remains unchanged.
-      \textit{Bottom}: using viscous boundary layers.
-      The four fmask parameters along the strait coastlines are set to a value larger than 4,
-      \ie "strong" no-slip case (see \autoref{fig:LBC_shlat}) creating a large viscous boundary layer that
-      allows a reduced transport through the strait.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=0.66\textwidth]{MISC_Gibraltar}
+  \includegraphics[width=0.66\textwidth]{MISC_Gibraltar2}
+  \caption[Two methods to defined the Gibraltar strait]{
+    Example of the Gibraltar strait defined in a 1\deg\ $\times$ 1\deg\ mesh.
+    \textit{Top}: using partially open cells.
+    The meridional scale factor at $v$-point is reduced on both sides of the strait to
+    account for the real width of the strait (about 20 km).
+    Note that the scale factors of the strait $T$-point remains unchanged.
+    \textit{Bottom}: using viscous boundary layers.
+    The four fmask parameters along the strait coastlines are set to a value larger than 4,
+    \ie\ "strong" no-slip case (see \autoref{fig:LBC_shlat}) creating a large viscous boundary layer
+    that allows a reduced transport through the strait.}
+  \label{fig:MISC_strait_hand}
 \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+
 \begin{figure}[!tbp]
-  \begin{center}
-    \includegraphics[width=1.0\textwidth]{Fig_closea_mask_example}
-    \caption{
-      \protect\label{fig:closea_mask_example}
-      Example of mask fields for the closea module. \textit{Left}: a
-      closea\_mask field; \textit{Right}: a closea\_mask\_rnf
-      field. In this example, if ln\_closea is set to .true., the mean
-      freshwater flux over each of the American Great Lakes will be
-      set to zero, and the total residual for all the lakes, if
-      negative, will be put into the St Laurence Seaway in the area
-      shown. 
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=0.66\textwidth]{MISC_closea_mask_example}
+  \caption[Mask fields for the \protect\mdl{closea} module]{
+    Example of mask fields for the \protect\mdl{closea} module.
+    \textit{Left}: a closea\_mask field;
+    \textit{Right}: a closea\_mask\_rnf field.
+    In this example, if \protect\np{ln_closea}{ln\_closea} is set to \forcode{.true.},
+    the mean freshwater flux over each of the American Great Lakes will be set to zero,
+    and the total residual for all the lakes, if negative, will be put into
+    the St Laurence Seaway in the area shown.}
+  \label{fig:MISC_closea_mask_example}
 \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-
-% ================================================================
-% Closed seas
-% ================================================================
-\section{Closed seas (\protect\mdl{closea})}
+
+%% =================================================================================================
+\section[Closed seas (\textit{closea.F90})]{Closed seas (\protect\mdl{closea})}
 \label{sec:MISC_closea}
 
@@ -116 +138 @@
 to zero and put the residual flux into the ocean.
 
-Prior to NEMO 4 the locations of inland seas and lakes was set via
-hardcoded indices for various ORCA configurations. From NEMO 4 onwards
+Prior to \NEMO\ 4 the locations of inland seas and lakes was set via
+hardcoded indices for various ORCA configurations. From \NEMO\ 4 onwards
 the inland seas and lakes are defined using mask fields in the
 domain configuration file. The options are as follows.
 
 \begin{enumerate}
-\item{{\bf No ``closea\_mask'' field is included in domain configuration
+\item {{\bfseries No ``closea\_mask'' field is included in domain configuration
   file.} In this case the closea module does nothing.}
 
-\item{{\bf A field called closea\_mask is included in the domain
+\item {{\bfseries A field called closea\_mask is included in the domain
 configuration file and ln\_closea=.false. in namelist namcfg.} In this
 case the inland seas defined by the closea\_mask field are filled in
@@ -131 +153 @@
 closea\_mask that is nonzero is set to be a land point.}
 
-\item{{\bf A field called closea\_mask is included in the domain
+\item {{\bfseries A field called closea\_mask is included in the domain
 configuration file and ln\_closea=.true. in namelist namcfg.} Each
 inland sea or group of inland seas is set to a positive integer value
-in the closea\_mask field (see Figure \ref{fig:closea_mask_example}
+in the closea\_mask field (see \autoref{fig:MISC_closea_mask_example}
 for an example). The net surface flux over each inland sea or group of
 inland seas is set to zero each timestep and the residual flux is
@@ -140 +162 @@
 closea\_mask is zero).}
 
-\item{{\bf Fields called closea\_mask and closea\_mask\_rnf are
+\item {{\bfseries Fields called closea\_mask and closea\_mask\_rnf are
 included in the domain configuration file and ln\_closea=.true. in
 namelist namcfg.} This option works as for option 3, except that if
@@ -149 +171 @@
 by the closea\_mask\_rnf field. Each mapping is defined by a positive
 integer value for the inland sea(s) and the corresponding runoff
-points. An example is given in Figure
-\ref{fig:closea_mask_example}. If no mapping is provided for a
+points. An example is given in
+\autoref{fig:MISC_closea_mask_example}. If no mapping is provided for a
 particular inland sea then the residual is spread over the global
 ocean.}
 
-\item{{\bf Fields called closea\_mask and closea\_mask\_emp are
+\item {{\bfseries Fields called closea\_mask and closea\_mask\_emp are
 included in the domain configuration file and ln\_closea=.true. in
 namelist namcfg.} This option works the same as option 4 except that
@@ -164 +186 @@
 
 There is a python routine to create the closea\_mask fields and append
-them to the domain configuration file in the utils/tools/DOMAINcfg directory. 
-
-% ================================================================
-% Sub-Domain Functionality 
-% ================================================================
+them to the domain configuration file in the utils/tools/DOMAINcfg directory.
+
+%% =================================================================================================
 \section{Sub-domain functionality}
 \label{sec:MISC_zoom}
 
+%% =================================================================================================
 \subsection{Simple subsetting of input files via NetCDF attributes}
 
-The extended grids for use with the under-shelf ice cavities will result in redundant rows around Antarctica if
-the ice cavities are not active.
-A simple mechanism for subsetting input files associated with the extended domains has been implemented to
-avoid the need to maintain different sets of input fields for use with or without active ice cavities.
-The existing 'zoom' options are overly complex for this task and marked for deletion anyway.
-This alternative subsetting operates for the j-direction only and works by optionally looking for and
-using a global file attribute (named: \np{open\_ocean\_jstart}) to determine the starting j-row for input.
-The use of this option is best explained with an example:
-consider an ORCA1 configuration using the extended grid bathymetry and coordinate files:
-\vspace{-10pt}
-\ifile{eORCA1\_bathymetry\_v2}
-\ifile{eORCA1\_coordinates}
-\noindent These files define a horizontal domain of 362x332.
-Assuming the first row with open ocean wet points in the non-isf bathymetry for this set is row 42
-(\fortran indexing) then the formally correct setting for \np{open\_ocean\_jstart} is 41.
-Using this value as the first row to be read will result in a 362x292 domain which is the same size as
-the original ORCA1 domain.
-Thus the extended coordinates and bathymetry files can be used with all the original input files for ORCA1 if
-the ice cavities are not active (\np{ln\_isfcav = .false.}).
-Full instructions for achieving this are:
-
-\noindent Add the new attribute to any input files requiring a j-row offset, i.e:
-\vspace{-10pt}
+The extended grids for use with the under-shelf ice cavities will result in redundant rows
+around Antarctica if the ice cavities are not active.  A simple mechanism for subsetting
+input files associated with the extended domains has been implemented to avoid the need to
+maintain different sets of input fields for use with or without active ice cavities.  This
+subsetting operates for the j-direction only and works by optionally looking for and using
+a global file attribute (named: \np{open_ocean_jstart}{open\_ocean\_jstart}) to determine the starting j-row
+for input.  The use of this option is best explained with an example:
+\medskip
+
+\noindent Consider an ORCA1
+configuration using the extended grid domain configuration file: \ifile{eORCA1\_domcfg.nc}
+This file define a horizontal domain of 362x332.  The first row with
+open ocean wet points in the non-isf bathymetry for this set is row 42 (\fortran\ indexing)
+then the formally correct setting for \np{open_ocean_jstart}{open\_ocean\_jstart} is 41.  Using this value as
+the first row to be read will result in a 362x292 domain which is the same size as the
+original ORCA1 domain.  Thus the extended domain configuration file can be used with all
+the original input files for ORCA1 if the ice cavities are not active (\np{ln\_isfcav =
+.false.}).  Full instructions for achieving this are:
+
+\begin{itemize}
+\item Add the new attribute to any input files requiring a j-row offset, i.e:
 \begin{cmds}
-ncatted  -a open_ocean_jstart,global,a,d,41 eORCA1_coordinates.nc 
-ncatted  -a open_ocean_jstart,global,a,d,41 eORCA1_bathymetry_v2.nc
+ncatted  -a open_ocean_jstart,global,a,d,41 eORCA1_domcfg.nc
 \end{cmds}
- 
-\noindent Add the logical switch to \ngn{namcfg} in the configuration namelist and set true:
-%--------------------------------------------namcfg--------------------------------------------------------
-
-\nlst{namcfg}
-%--------------------------------------------------------------------------------------------------------------
-
-\noindent Note the j-size of the global domain is the (extended j-size minus \np{open\_ocean\_jstart} + 1 ) and
-this must match the size of all datasets other than bathymetry and coordinates currently.
-However the option can be extended to any global, 2D and 3D, netcdf, input field by adding the:
-\vspace{-10pt}
+
+\item Add the logical switch \np{ln_use_jattr}{ln\_use\_jattr} to \nam{cfg}{cfg} in the configuration
+namelist (if it is not already there) and set \forcode{.true.}
+\end{itemize}
+
+\noindent Note that with this option, the j-size of the global domain is (extended
+j-size minus \np{open_ocean_jstart}{open\_ocean\_jstart} + 1 ) and this must match the \texttt{jpjglo} value
+for the configuration. This means an alternative version of \ifile{eORCA1\_domcfg.nc} must
+be created for when \np{ln_use_jattr}{ln\_use\_jattr} is active. The \texttt{ncap2} tool provides a
+convenient way of achieving this:
+
+\begin{cmds}
+ncap2 -s 'jpjglo=292' eORCA1_domcfg.nc nORCA1_domcfg.nc
+\end{cmds}
+
+The domain configuration file is unique in this respect since it also contains the value of \jp{jpjglo}
+that is read and used by the model.
+Any other global, 2D and 3D, netcdf, input field can be prepared for use in a reduced domain by adding the
+\texttt{open\_ocean\_jstart} attribute to the file's global attributes.
+In particular this is true for any field that is read by \NEMO\ using the following optional argument to
+the appropriate call to \np{iom_get}{iom\_get}.
+
 \begin{forlines}
 lrowattr=ln_use_jattr
 \end{forlines}
-optional argument to the appropriate \np{iom\_get} call and the \np{open\_ocean\_jstart} attribute to
-the corresponding input files.
-It remains the users responsibility to set \np{jpjdta} and \np{jpjglo} values in
-the \np{namelist\_cfg} file according to their needs.
-
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-\begin{figure}[!ht]
-  \begin{center}
-    \includegraphics[width=0.90\textwidth]{Fig_LBC_zoom}
-    \caption{
-      \protect\label{fig:LBC_zoom}
-      Position of a model domain compared to the data input domain when the zoom functionality is used.
-    }
-  \end{center}
-\end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-
-
-% ================================================================
-% Accuracy and Reproducibility
-% ================================================================
-\section{Accuracy and reproducibility (\protect\mdl{lib\_fortran})}
+
+Currently, only the domain configuration variables make use of this optional argument so
+this facility is of little practical use except for tests where no other external input
+files are needed or you wish to use an extended domain configuration with inputs from
+earlier, non-extended configurations. Alternatively, it should be possible to exclude
+empty rows for extended domain, forced ocean runs using interpolation on the fly, by
+adding the optional argument to \texttt{iom\_get} calls for the weights and initial
+conditions. Experimenting with this remains an exercise for the user.
+
+%% =================================================================================================
+\section[Accuracy and reproducibility (\textit{lib\_fortran.F90})]{Accuracy and reproducibility (\protect\mdl{lib\_fortran})}
 \label{sec:MISC_fortran}
 
-\subsection{Issues with intrinsinc SIGN function (\protect\key{nosignedzero})}
+%% =================================================================================================
+\subsection[Issues with intrinsinc SIGN function (\texttt{\textbf{key\_nosignedzero}})]{Issues with intrinsinc SIGN function (\protect\key{nosignedzero})}
 \label{subsec:MISC_sign}
 
-The SIGN(A, B) is the \fortran intrinsic function delivers the magnitude of A with the sign of B.
+The SIGN(A, B) is the \fortran\ intrinsic function delivers the magnitude of A with the sign of B.
 For example, SIGN(-3.0,2.0) has the value 3.0.
 The problematic case is when the second argument is zero, because, on platforms that support IEEE arithmetic,
@@ -254 +273 @@
 and the processor is capable of distinguishing between positive and negative zero,
 and B is negative real zero.
-Then SIGN delivers a negative result where, under \fninety rules, it used to return a positive result.
+Then SIGN delivers a negative result where, under \fninety\ rules, it used to return a positive result.
 This change may be especially sensitive for the ice model,
 so we overwrite the intrinsinc function with our own function simply performing :   \\
@@ -264 +283 @@
 some computers/compilers.
 
-
+%% =================================================================================================
 \subsection{MPP reproducibility}
 \label{subsec:MISC_glosum}
 
 The numerical reproducibility of simulations on distributed memory parallel computers is a critical issue.
-In particular, within NEMO global summation of distributed arrays is most susceptible to rounding errors,
+In particular, within \NEMO\ global summation of distributed arrays is most susceptible to rounding errors,
 and their propagation and accumulation cause uncertainty in final simulation reproducibility on
 different numbers of processors.
-To avoid so, based on \citet{He_Ding_JSC01} review of different technics,
+To avoid so, based on \citet{he.ding_JS01} review of different technics,
 we use a so called self-compensated summation method.
-The idea is to estimate the roundoff error, store it in a buffer, and then add it back in the next addition. 
+The idea is to estimate the roundoff error, store it in a buffer, and then add it back in the next addition.
 
 Suppose we need to calculate $b = a_1 + a_2 + a_3$.
@@ -292 +311 @@
 The self-compensated summation method should be used in all summation in i- and/or j-direction.
 See \mdl{closea} module for an example.
-Note also that this implementation may be sensitive to the optimization level. 
-
+Note also that this implementation may be sensitive to the optimization level.
+
+%% =================================================================================================
 \subsection{MPP scalability}
 \label{subsec:MISC_mppsca}
@@ -313 +333 @@
 be set at all the locations actually required by each individual for the fold operation.
 This alternative method should give identical results to the default \textsc{ALLGATHER} method and
-is recommended for large values of \np{jpni}.
-The new method is activated by setting \np{ln\_nnogather} to be true ({\bf nammpp}).
+is recommended for large values of \np{jpni}{jpni}.
+The new method is activated by setting \np{ln_nnogather}{ln\_nnogather} to be true (\nam{mpp}{mpp}).
 The reproducibility of results using the two methods should be confirmed for each new,
 non-reference configuration.
 
-% ================================================================
-% Model optimisation, Control Print and Benchmark
-% ================================================================
+%% =================================================================================================
 \section{Model optimisation, control print and benchmark}
 \label{sec:MISC_opt}
-%--------------------------------------------namctl-------------------------------------------------------
-
-\nlst{namctl} 
-%--------------------------------------------------------------------------------------------------------------
-
-Options are defined through the  \ngn{namctl} namelist variables.
-
+
+\begin{listing}
+  \nlst{namctl}
+  \caption{\forcode{&namctl}}
+  \label{lst:namctl}
+\end{listing}
+
+Options are defined through the  \nam{ctl}{ctl} namelist variables.
+
+%% =================================================================================================
 \subsection{Vector optimisation}
 
@@ -335 +356 @@
 This is very a very efficient way to increase the length of vector calculations and thus
 to speed up the model on vector computers.
- 
+
 % Add here also one word on NPROMA technique that has been found useless, since compiler have made significant progress during the last decade.
- 
+
 % Add also one word on NEC specific optimisation (Novercheck option for example)
- 
+
+%% =================================================================================================
 \subsection{Control print}
 
-The \np{ln\_ctl} switch was originally used as a debugging option in two modes:
+The \np{ln_ctl}{ln\_ctl} switch was originally used as a debugging option in two modes:
 
 \begin{enumerate}
-\item{\np{ln\_ctl}: compute and print the trends averaged over the interior domain in all TRA, DYN, LDF and
+\item {\np{ln_ctl}{ln\_ctl}: compute and print the trends averaged over the interior domain in all TRA, DYN, LDF and
 ZDF modules.
 This option is very helpful when diagnosing the origin of an undesired change in model results. }
 
-\item{also \np{ln\_ctl} but using the nictl and njctl namelist parameters to check the source of differences between
+\item {also \np{ln_ctl}{ln\_ctl} but using the nictl and njctl namelist parameters to check the source of differences between
 mono and multi processor runs.}
 \end{enumerate}
 
 However, in recent versions it has also been used to force all processors to assume the
-reporting role. Thus when \np{ln\_ctl} is true all processors produce their own versions
+reporting role. Thus when \np{ln_ctl}{ln\_ctl} is true all processors produce their own versions
 of files such as: ocean.output, layout.dat, etc.  All such files, beyond the the normal
 reporting processor (narea == 1), are named with a \_XXXX extension to their name, where
@@ -360 +382 @@
 such as run.stat (and its netCDF counterpart: run.stat.nc) and tracer.stat contain global
 information and are only ever produced by the reporting master (narea == 1). For version
-4.0 a start has been made to return \np{ln\_ctl} to its original function by introducing
+4.0 a start has been made to return \np{ln_ctl}{ln\_ctl} to its original function by introducing
 a new control structure which allows finer control over which files are produced. This
 feature is still evolving but it does already allow the user to: select individually the
@@ -386 +408 @@
 at a suitably long interval. For example:
 
-\begin{verbatim}     
+\begin{verbatim}
        sn_cfctl%ptimincr  = 25
 \end{verbatim}
 
-will carry out the global communications and write the information every 25 timesteps. This 
+will carry out the global communications and write the information every 25 timesteps. This
 increment also applies to the time.step file which is otherwise updated every timestep.
 
-% ================================================================
-\biblio
-
-\pindex
+\subinc{\input{../../global/epilogue}}
 
 \end{document}

@@ -1 @@
-*.aux
-*.bbl
-*.blg
-*.dvi
-*.fdb*
-*.fls
-*.idx
+*.ind
 *.ilg
-*.ind
-*.log
-*.maf
-*.mtc*
-*.out
-*.pdf
-*.toc
-_minted-*