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

Timestamp:

2019-10-25T16:27:34+02:00 (4 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:

• . (modified) (1 prop)
• latex (modified) (1 prop)
• latex/NEMO (modified) (1 prop)
• latex/NEMO/subfiles (modified) (1 prop)
• latex/NEMO/subfiles/chap_OBS.tex (modified) (42 diffs)

NEMO/branches/2019/dev_r11470_HPC_12_mpi3/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_r11470_HPC_12_mpi3/doc/latex/NEMO/subfiles/chap_OBS.tex

@@ -2 +2 @@
 
 \begin{document}
-% ================================================================
-% Chapter observation operator (OBS)
-% ================================================================
+
 \chapter{Observation and Model Comparison (OBS)}
 \label{chap:OBS}
 
+%\subsubsection*{Changes record}
+%\begin{tabular}{l||l|m{0.65\linewidth}}
+%    Release   & Author        & Modifications \\
+%    {\em 4.0} & {\em D. J. Lea} & {\em \NEMO\ 4.0 updates}  \\
+%    {\em 3.6} & {\em M. Martin, A. Ryan} & {\em Add averaging operator, standalone obs oper} \\
+%    {\em 3.4} & {\em D. J. Lea, M. Martin, ...} & {\em Initial version}  \\
+%    {\em --\texttt{"}--} & {\em ... K. Mogensen, A. Vidard, A. Weaver} & {\em ---\texttt{"}---}  \\
+%\end{tabular}
+
+\thispagestyle{plain}
+
 \chaptertoc
 
-\vfill
-\begin{figure}[b]
-\subsubsection*{Changes record}
-\begin{tabular}{l||l|m{0.65\linewidth}}
-    Release   & Author        & Modifications \\
-    {\em 4.0} & {\em D. J. Lea} & {\em \NEMO\ 4.0 updates}  \\
-    {\em 3.6} & {\em M. Martin, A. Ryan} & {\em Add averaging operator, standalone obs oper} \\
-    {\em 3.4} & {\em D. J. Lea, M. Martin, ...} & {\em Initial version}  \\
-    {\em --\texttt{"}--} & {\em ... K. Mogensen, A. Vidard, A. Weaver} & {\em ---\texttt{"}---}  \\
-\end{tabular}
-\end{figure}
-
-\newpage
+\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
 
 The observation and model comparison code, the observation operator (OBS), reads in observation files
@@ -32 +42 @@
 The OBS code is called from \mdl{nemogcm} for model initialisation and to calculate the model equivalent values for observations on the 0th time step.
 The code is then called again after each time step from \mdl{step}.
-The code is only activated if the \nam{obs} namelist logical \np{ln\_diaobs} is set to true.
+The code is only activated if the \nam{obs}{obs} namelist logical \np{ln_diaobs}{ln\_diaobs} is set to true.
 
 For all data types a 2D horizontal interpolator or averager is needed to
@@ -42 +52 @@
 Some profile observation types (\eg\ tropical moored buoys) are made available as daily averaged quantities.
 The observation operator code can be set-up to calculate the equivalent daily average model temperature fields using
-the \np{nn\_profdavtypes} namelist array.
+the \np{nn_profdavtypes}{nn\_profdavtypes} namelist array.
 Some SST observations are equivalent to a night-time average value and
 the observation operator code can calculate equivalent night-time average model SST fields by
-setting the namelist value \np{ln\_sstnight} to true.
+setting the namelist value \np{ln_sstnight}{ln\_sstnight} to true.
 Otherwise (by default) the model value from the nearest time step to the observation time is used.
 
-The code is controlled by the namelist \nam{obs}.
+The code is controlled by the namelist \nam{obs}{obs}.
 See the following sections for more details on setting up the namelist.
 
@@ -60 +70 @@
 In \autoref{sec:OBS_obsutils} we describe some utilities to help work with the files produced by the OBS code.
 
-% ================================================================
-% Example
-% ================================================================
+%% =================================================================================================
 \section{Running the observation operator code example}
 \label{sec:OBS_example}
@@ -92 +100 @@
 \end{enumerate}
 
-Options are defined through the \nam{obs} namelist variables.
-The options \np{ln\_t3d} and \np{ln\_s3d} switch on the temperature and salinity profile observation operator code.
-The filename or array of filenames are specified using the \np{cn\_profbfiles} variable.
+Options are defined through the \nam{obs}{obs} namelist variables.
+The options \np{ln_t3d}{ln\_t3d} and \np{ln_s3d}{ln\_s3d} switch on the temperature and salinity profile observation operator code.
+The filename or array of filenames are specified using the \np{cn_profbfiles}{cn\_profbfiles} variable.
 The model grid points for a particular observation latitude and longitude are found using
 the grid searching part of the code.
 This can be expensive, particularly for large numbers of observations,
-setting \np{ln\_grid\_search\_lookup} allows the use of a lookup table which
-is saved into an \np{cn\_gridsearch} file (or files).
+setting \np{ln_grid_search_lookup}{ln\_grid\_search\_lookup} allows the use of a lookup table which
+is saved into an \np{cn_gridsearch}{cn\_gridsearch} file (or files).
 This will need to be generated the first time if it does not exist in the run directory.
 However, once produced it will significantly speed up future grid searches.
-Setting \np{ln\_grid\_global} means that the code distributes the observations evenly between processors.
+Setting \np{ln_grid_global}{ln\_grid\_global} means that the code distributes the observations evenly between processors.
 Alternatively each processor will work with observations located within the model subdomain
 (see \autoref{subsec:OBS_parallel}).
@@ -111 +119 @@
 \autoref{sec:OBS_obsutils}.
 
+%% =================================================================================================
 \section{Technical details (feedback type observation file headers)}
 \label{sec:OBS_details}
 
-Here we show a more complete example namelist \nam{obs} and also show the NetCDF headers of
+Here we show a more complete example namelist \nam{obs}{obs} and also show the NetCDF headers of
 the observation files that may be used with the observation operator.
 
-%------------------------------------------namobs--------------------------------------------------------
-
-\nlst{namobs}
-%-------------------------------------------------------------------------------------------------------------
+\begin{listing}
+  \nlst{namobs}
+  \caption{\forcode{&namobs}}
+  \label{lst:namobs}
+\end{listing}
 
 The observation operator code uses the feedback observation file format for all data types.
@@ -127 +137 @@
 sea surface temperature are in the following subsections.
 
+%% =================================================================================================
 \subsection{Profile feedback file}
 
@@ -283 +294 @@
 \end{clines}
 
+%% =================================================================================================
 \subsection{Sea level anomaly feedback file}
 
@@ -429 +441 @@
 \end{clines}
 
+%% =================================================================================================
 \subsection{Sea surface temperature feedback file}
 
@@ -546 +559 @@
 \end{clines}
 
+%% =================================================================================================
 \section{Theoretical details}
 \label{sec:OBS_theory}
 
+%% =================================================================================================
 \subsection{Horizontal interpolation and averaging methods}
 
@@ -561 +576 @@
 (for surface observation types only).
 
-The main namelist option associated with the interpolation/averaging is \np{nn\_2dint}.
+The main namelist option associated with the interpolation/averaging is \np{nn_2dint}{nn\_2dint}.
 This default option can be set to values from 0 to 6.
 Values between 0 to 4 are associated with interpolation while values 5 or 6 are associated with averaging.
 \begin{itemize}
-\item \np{nn\_2dint}\forcode{ = 0}: Distance-weighted interpolation
-\item \np{nn\_2dint}\forcode{ = 1}: Distance-weighted interpolation (small angle)
-\item \np{nn\_2dint}\forcode{ = 2}: Bilinear interpolation (geographical grid)
-\item \np{nn\_2dint}\forcode{ = 3}: Bilinear remapping interpolation (general grid)
-\item \np{nn\_2dint}\forcode{ = 4}: Polynomial interpolation
-\item \np{nn\_2dint}\forcode{ = 5}: Radial footprint averaging with diameter specified in the namelist as
+\item \np[=0]{nn_2dint}{nn\_2dint}: Distance-weighted interpolation
+\item \np[=1]{nn_2dint}{nn\_2dint}: Distance-weighted interpolation (small angle)
+\item \np[=2]{nn_2dint}{nn\_2dint}: Bilinear interpolation (geographical grid)
+\item \np[=3]{nn_2dint}{nn\_2dint}: Bilinear remapping interpolation (general grid)
+\item \np[=4]{nn_2dint}{nn\_2dint}: Polynomial interpolation
+\item \np[=5]{nn_2dint}{nn\_2dint}: Radial footprint averaging with diameter specified in the namelist as
   \texttt{rn\_[var]\_avglamscl} in degrees or metres (set using \texttt{ln\_[var]\_fp\_indegs})
-\item \np{nn\_2dint}\forcode{ = 6}: Rectangular footprint averaging with E/W and N/S size specified in
+\item \np[=6]{nn_2dint}{nn\_2dint}: Rectangular footprint averaging with E/W and N/S size specified in
   the namelist as \texttt{rn\_[var]\_avglamscl} and \texttt{rn\_[var]\_avgphiscl} in degrees or metres
   (set using \texttt{ln\_[var]\_fp\_indegs})
@@ -578 +593 @@
 Replace \texttt{[var]} in the last two options with the observation type (sla, sst, sss or sic) for
 which the averaging is to be performed (see namelist example above).
-The \np{nn\_2dint} default option can be overridden for surface observation types using
+The \np{nn_2dint}{nn\_2dint} default option can be overridden for surface observation types using
 namelist values \texttt{nn\_2dint\_[var]} where \texttt{[var]} is the observation type.
 
 Below is some more detail on the various options for interpolation and averaging available in \NEMO.
 
+%% =================================================================================================
 \subsubsection{Horizontal interpolation}
 
@@ -605 +621 @@
 
 \begin{enumerate}
-
-\item[1.] {\bfseries Great-Circle distance-weighted interpolation.}
+\item {\bfseries Great-Circle distance-weighted interpolation.}
   The weights are computed as a function of the great-circle distance $s(P, \cdot)$ between $P$ and
   the model grid points $A$, $B$ etc.
@@ -651 +666 @@
    \end{alignat*}
 
-\item[2.] {\bfseries Great-Circle distance-weighted interpolation with small angle approximation.}
+\item {\bfseries Great-Circle distance-weighted interpolation with small angle approximation.}
   Similar to the previous interpolation but with the distance $s$ computed as
   \begin{alignat*}{2}
@@ -661 +676 @@
   where $M$ corresponds to $A$, $B$, $C$ or $D$.
 
-\item[3.] {\bfseries Bilinear interpolation for a regular spaced grid.}
+\item {\bfseries Bilinear interpolation for a regular spaced grid.}
   The interpolation is split into two 1D interpolations in the longitude and latitude directions, respectively.
 
-\item[4.] {\bfseries Bilinear remapping interpolation for a general grid.}
+\item {\bfseries Bilinear remapping interpolation for a general grid.}
   An iterative scheme that involves first mapping a quadrilateral cell into
   a cell with coordinates (0,0), (1,0), (0,1) and (1,1).
@@ -671 +686 @@
 \end{enumerate}
 
+%% =================================================================================================
 \subsubsection{Horizontal averaging}
 
@@ -691 +707 @@
 
 Examples of the weights calculated for an observation with rectangular and radial footprints are shown in
-\autoref{fig:obsavgrec} and~\autoref{fig:obsavgrad}.
-
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+\autoref{fig:OBS_avgrec} and~\autoref{fig:OBS_avgrad}.
+
 \begin{figure}
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_OBS_avg_rec}
-    \caption{
-      \protect\label{fig:obsavgrec}
-      Weights associated with each model grid box (blue lines and numbers)
-      for an observation at -170.5\deg{E}, 56.0\deg{N} with a rectangular footprint of 1\deg x 1\deg.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=0.66\textwidth]{Fig_OBS_avg_rec}
+  \caption[Observational weights with a rectangular footprint]{
+    Weights associated with each model grid box (blue lines and numbers)
+    for an observation at -170.5\deg{E}, 56.0\deg{N} with a rectangular footprint of 1\deg\ x 1\deg.}
+  \label{fig:OBS_avgrec}
 \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+
 \begin{figure}
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_OBS_avg_rad}
-    \caption{
-      \protect\label{fig:obsavgrad}
-      Weights associated with each model grid box (blue lines and numbers)
-      for an observation at -170.5\deg{E}, 56.0\deg{N} with a radial footprint with diameter 1\deg.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=0.66\textwidth]{Fig_OBS_avg_rad}
+  \caption[Observational weights with a radial footprint]{
+    Weights associated with each model grid box (blue lines and numbers)
+    for an observation at -170.5\deg{E}, 56.0\deg{N} with a radial footprint with diameter 1\deg.}
+  \label{fig:OBS_avgrad}
 \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-
-
+
+%% =================================================================================================
 \subsection{Grid search}
 
@@ -756 +764 @@
           ({\phi_{}}_{\mathrm D}  \;  - \; {\phi_{}}_{\mathrm P} )] \; \widehat{\mathbf k} \\
   \end{array}
-  % \label{eq:cross}
+  % \label{eq:OBS_cross}
 \end{align*}
 point in the opposite direction to the unit normal $\widehat{\mathbf k}$
@@ -770 +778 @@
 the $i$ and $j$ ranges of this point searched to determine the precise four points surrounding the observation.
 
+%% =================================================================================================
 \subsection{Parallel aspects of horizontal interpolation}
 \label{subsec:OBS_parallel}
@@ -784 +793 @@
 and 2) round-robin.
 
+%% =================================================================================================
 \subsubsection{Geographical distribution of observations among processors}
 
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_ASM_obsdist_local}
-    \caption{
-      \protect\label{fig:obslocal}
-      Example of the distribution of observations with the geographical distribution of observational data.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=0.66\textwidth]{Fig_ASM_obsdist_local}
+  \caption[Observations with the geographical distribution]{
+    Example of the distribution of observations with
+    the geographical distribution of observational data}
+  \label{fig:OBS_local}
 \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
 This is the simplest option in which the observations are distributed according to
 the domain of the grid-point parallelization.
-\autoref{fig:obslocal} shows an example of the distribution of the {\em in situ} data on processors with
+\autoref{fig:OBS_local} shows an example of the distribution of the {\em in situ} data on processors with
 a different colour for each observation on a given processor for a 4 $\times$ 2 decomposition with ORCA2.
 The grid-point domain decomposition is clearly visible on the plot.
@@ -813 +820 @@
 this could lead to load imbalance.
 
+%% =================================================================================================
 \subsubsection{Round-robin distribution of observations among processors}
 
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_ASM_obsdist_global}
-    \caption{
-      \protect\label{fig:obsglobal}
-      Example of the distribution of observations with the round-robin distribution of observational data.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=0.66\textwidth]{Fig_ASM_obsdist_global}
+  \caption[Observations with the round-robin distribution]{
+    Example of the distribution of observations with
+    the round-robin distribution of observational data.}
+  \label{fig:OBS_global}
 \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
 An alternative approach is to distribute the observations equally among processors and
 use message passing in order to retrieve the stencil for interpolation.
 The simplest distribution of the observations is to distribute them using a round-robin scheme.
-\autoref{fig:obsglobal} shows the distribution of the {\em in situ} data on processors for
+\autoref{fig:OBS_global} shows the distribution of the {\em in situ} data on processors for
 the round-robin distribution of observations with a different colour for each observation on a given processor for
-a 4 $\times$ 2 decomposition with ORCA2 for the same input data as in \autoref{fig:obslocal}.
+a 4 $\times$ 2 decomposition with ORCA2 for the same input data as in \autoref{fig:OBS_local}.
 The observations are now clearly randomly distributed on the globe.
 In order to be able to perform horizontal interpolation in this case,
 a subroutine has been developed that retrieves any grid points in the global space.
 
+%% =================================================================================================
 \subsection{Vertical interpolation operator}
 
@@ -846 +852 @@
 For profile observation types we do both vertical and horizontal interpolation. \NEMO\ has a generalised vertical coordinate system this means the vertical level depths can vary with location. Therefore, it is necessary first to perform vertical interpolation of the model value to the observation depths for each of the four surrounding grid points. After this the model values, at these points, at the observation depth, are horizontally interpolated to the observation location.
 
-\newpage
-
-% ================================================================
-% Standalone observation operator documentation
-% ================================================================
-
 %\usepackage{framed}
 
+%% =================================================================================================
 \section{Standalone observation operator}
 \label{sec:OBS_sao}
 
+%% =================================================================================================
 \subsection{Concept}
 
@@ -873 +875 @@
 By forecast, we mean any method which produces an estimate of physical reality which is not an observed value.
 
-%--------------------------------------------------------------------------------------------------------
 % sao.exe
-%--------------------------------------------------------------------------------------------------------
-
+
+%% =================================================================================================
 \subsection{Using the standalone observation operator}
 
+%% =================================================================================================
 \subsubsection{Building}
 
@@ -886 +888 @@
 Note this a similar approach to that taken by the standalone surface scheme \emph{SAS\_SRC} and the offline TOP model \emph{OFF\_SRC}.
 
-%--------------------------------------------------------------------------------------------------------
 % Running
-%--------------------------------------------------------------------------------------------------------
+%% =================================================================================================
 \subsubsection{Running}
 
@@ -894 +895 @@
 a full \NEMO\ namelist and then to run the executable as if it were nemo.exe.
 
-%--------------------------------------------------------------------------------------------------------
 % Configuration section
-%--------------------------------------------------------------------------------------------------------
+%% =================================================================================================
 \subsection{Configuring the standalone observation operator}
-The observation files and settings understood by \nam{obs} have been outlined in the online observation operator section.
-In addition is a further namelist \nam{sao} which used to set the input model fields for the SAO
-
+The observation files and settings understood by \nam{obs}{obs} have been outlined in the online observation operator section.
+In addition is a further namelist \nam{sao}{sao} which used to set the input model fields for the SAO
+
+%% =================================================================================================
 \subsubsection{Single field}
 
@@ -909 +910 @@
 \textbf{votemper}, \textbf{vosaline} and optionally \textbf{sshn} present.
 
-For each field read there must be an entry in the \nam{sao} namelist specifying
+For each field read there must be an entry in the \nam{sao}{sao} namelist specifying
 the name of the file to read and the index along the \emph{time\_counter}.
 For example, to read the second time counter from a single file the namelist would be.
@@ -925 +926 @@
 \end{forlines}
 
+%% =================================================================================================
 \subsubsection{Multiple fields per run}
 
@@ -960 +962 @@
 This approach is referred to as \emph{Class 4} since it is the fourth metric defined by the GODAE intercomparison project. This requires multiple runs of the SAO and running an additional utility (not currently in the \NEMO\ repository) to combine the feedback files into one class 4 file.
 
-\newpage
-
+%% =================================================================================================
 \section{Observation utilities}
 \label{sec:OBS_obsutils}
@@ -967 +968 @@
 For convenience some tools for viewing and processing of observation and feedback files are provided in
 the \NEMO\ repository.
-These tools include OBSTOOLS which are a collection of \fortran programs which are helpful to deal with feedback files.
+These tools include OBSTOOLS which are a collection of \fortran\ programs which are helpful to deal with feedback files.
 They do such tasks as observation file conversion, printing of file contents,
 some basic statistical analysis of feedback files.
@@ -974 +975 @@
 OBSTOOLS and dataplot are described in more detail below.
 
+%% =================================================================================================
 \subsection{Obstools}
 
-A series of \fortran utilities is provided with \NEMO\ called OBSTOOLS.
+A series of \fortran\ utilities is provided with \NEMO\ called OBSTOOLS.
 This are helpful in handling observation files and the feedback file output from the observation operator. A brief description of some of the utilities follows
 
+%% =================================================================================================
 \subsubsection{corio2fb}
 
@@ -988 +991 @@
 \end{cmds}
 
+%% =================================================================================================
 \subsubsection{enact2fb}
 
@@ -997 +1001 @@
 \end{cmds}
 
+%% =================================================================================================
 \subsubsection{fbcomb}
 
@@ -1007 +1012 @@
 \end{cmds}
 
+%% =================================================================================================
 \subsubsection{fbmatchup}
 
@@ -1016 +1022 @@
 \end{cmds}
 
+%% =================================================================================================
 \subsubsection{fbprint}
 
@@ -1044 +1051 @@
 \end{cmds}
 
+%% =================================================================================================
 \subsubsection{fbsel}
 
@@ -1053 +1061 @@
 \end{cmds}
 
+%% =================================================================================================
 \subsubsection{fbstat}
 
@@ -1062 +1071 @@
 \end{cmds}
 
+%% =================================================================================================
 \subsubsection{fbthin}
 
@@ -1072 +1082 @@
 \end{cmds}
 
+%% =================================================================================================
 \subsubsection{sla2fb}
 
@@ -1084 +1095 @@
 \end{cmds}
 
+%% =================================================================================================
 \subsubsection{vel2fb}
 
@@ -1093 +1105 @@
 \end{cmds}
 
+%% =================================================================================================
 \subsection{Building the obstools}
 
 To build the obstools use in the tools directory use ./maketools -n OBSTOOLS -m [ARCH].
 
+%% =================================================================================================
 \subsection{Dataplot}
 
@@ -1118 +1132 @@
 \end{minted}
 
-\autoref{fig:obsdataplotmain} shows the main window which is launched when dataplot starts.
+\autoref{fig:OBS_dataplotmain} shows the main window which is launched when dataplot starts.
 This is split into three parts.
 At the top there is a menu bar which contains a variety of drop down menus.
@@ -1148 +1162 @@
 The rightmost group of buttons will print the plot window as a postscript, save it as png, or exit from dataplot.
 
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}
-  \begin{center}
-    % \includegraphics[width=\textwidth]{Fig_OBS_dataplot_main}
-    \includegraphics[width=\textwidth]{Fig_OBS_dataplot_main}
-    \caption{
-      \protect\label{fig:obsdataplotmain}
-      Main window of dataplot.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=0.66\textwidth]{Fig_OBS_dataplot_main}
+  \caption{Main window of dataplot}
+  \label{fig:OBS_dataplotmain}
 \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
 If a profile point is clicked with the mouse button a plot of the observation and background values as
-a function of depth (\autoref{fig:obsdataplotprofile}).
-
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+a function of depth (\autoref{fig:OBS_dataplotprofile}).
+
 \begin{figure}
-  \begin{center}
-    % \includegraphics[width=\textwidth]{Fig_OBS_dataplot_prof}
-    \includegraphics[width=\textwidth]{Fig_OBS_dataplot_prof}
-    \caption{
-      \protect\label{fig:obsdataplotprofile}
-      Profile plot from dataplot produced by right clicking on a point in the main window.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=0.66\textwidth]{Fig_OBS_dataplot_prof}
+  \caption[Profile plot from dataplot]{
+    Profile plot from dataplot produced by right clicking on a point in the main window}
+  \label{fig:OBS_dataplotprofile}
 \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-
-\biblio
-
-\pindex
+
+\onlyinsubfile{\input{../../global/epilogue}}
 
 \end{document}

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