Changeset 11692 for NEMO/branches/2019/dev_r11514_HPC-02_single-core-extrahalo/doc/latex/NEMO/subfiles/chap_LBC.tex

Timestamp:

2019-10-12T16:08:18+02:00 (5 years ago)

Author:

francesca

Message:

Update branch to integrate the development starting from the current v4.01 ready trunk

Location:

NEMO/branches/2019/dev_r11514_HPC-02_single-core-extrahalo/doc

Files:

• . (modified) (1 prop)
• latex (modified) (1 prop)
• latex/NEMO (modified) (1 prop)
• latex/NEMO/subfiles (modified) (1 prop)
• latex/NEMO/subfiles/chap_LBC.tex (modified) (30 diffs)

NEMO/branches/2019/dev_r11514_HPC-02_single-core-extrahalo/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_r11514_HPC-02_single-core-extrahalo/doc/latex/NEMO/subfiles/chap_LBC.tex

@@ -2 +2 @@
 
 \begin{document}
-% ================================================================
-% Chapter — Lateral Boundary Condition (LBC)
-% ================================================================
+
 \chapter{Lateral Boundary Condition (LBC)}
 \label{chap:LBC}
 
+\thispagestyle{plain}
+
 \chaptertoc
 
-\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
 
 %gm% add here introduction to this chapter
 
-% ================================================================
-% Boundary Condition at the Coast
-% ================================================================
-\section[Boundary condition at the coast (\texttt{rn\_shlat})]
-{Boundary condition at the coast (\protect\np{rn\_shlat})}
+%% =================================================================================================
+\section[Boundary condition at the coast (\forcode{rn_shlat})]{Boundary condition at the coast (\protect\np{rn_shlat}{rn\_shlat})}
 \label{sec:LBC_coast}
-%--------------------------------------------nam_lbc-------------------------------------------------------
-
-\nlst{namlbc}
-%--------------------------------------------------------------------------------------------------------------
+
+\begin{listing}
+  \nlst{namlbc}
+  \caption{\forcode{&namlbc}}
+  \label{lst:namlbc}
+\end{listing}
 
 %The lateral ocean boundary conditions contiguous to coastlines are Neumann conditions for heat and salt
@@ -40 +52 @@
 %The process of defining which areas are to be masked is described in \autoref{subsec:DOM_msk}.
 
-Options are defined through the \nam{lbc} namelist variables.
+Options are defined through the \nam{lbc}{lbc} namelist variables.
 The discrete representation of a domain with complex boundaries (coastlines and bottom topography) leads to
 arrays that include large portions where a computation is not required as the model variables remain at zero.
@@ -57 +69 @@
 
 \[
-  % \label{eq:lbc_aaaa}
+  % \label{eq:LBC_aaaa}
   \frac{A^{lT} }{e_1 }\frac{\partial T}{\partial i}\equiv \frac{A_u^{lT}
   }{e_{1u} } \; \delta_{i+1 / 2} \left[ T \right]\;\;mask_u
@@ -65 +77 @@
 (normal velocity $u$ remains zero at the coast) (\autoref{fig:LBC_uv}).
 
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_LBC_uv}
-    \caption{
-      \protect\label{fig:LBC_uv}
-      Lateral boundary (thick line) at T-level.
-      The velocity normal to the boundary is set to zero.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=0.66\textwidth]{LBC_uv}
+  \caption[Lateral boundary at $T$-level]{
+    Lateral boundary (thick line) at T-level.
+    The velocity normal to the boundary is set to zero.}
+  \label{fig:LBC_uv}
 \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
 For momentum the situation is a bit more complex as two boundary conditions must be provided along the coast
@@ -90 +98 @@
 and is required in order to compute the vorticity at the coast.
 Four different types of lateral boundary condition are available,
-controlled by the value of the \np{rn\_shlat} namelist parameter
+controlled by the value of the \np{rn_shlat}{rn\_shlat} namelist parameter
 (The value of the mask$_{f}$ array along the coastline is set equal to this parameter).
 These are:
 
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!p]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_LBC_shlat}
-    \caption{
-      \protect\label{fig:LBC_shlat}
-      lateral boundary condition
-      (a) free-slip ($rn\_shlat=0$);
-      (b) no-slip ($rn\_shlat=2$);
-      (c) "partial" free-slip ($0<rn\_shlat<2$) and
-      (d) "strong" no-slip ($2<rn\_shlat$).
-      Implied "ghost" velocity inside land area is display in grey.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=0.66\textwidth]{LBC_shlat}
+  \caption[Lateral boundary conditions]{
+    Lateral boundary conditions
+    (a) free-slip                       (\protect\np[=0]{rn_shlat}{rn\_shlat});
+    (b) no-slip                         (\protect\np[=2]{rn_shlat}{rn\_shlat});
+    (c) "partial" free-slip (\forcode{0<}\protect\np[<2]{rn_shlat}{rn\_shlat}) and
+    (d) "strong" no-slip    (\forcode{2<}\protect\np{rn_shlat}{rn\_shlat}).
+    Implied "ghost" velocity inside land area is display in grey.}
+  \label{fig:LBC_shlat}
 \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
 \begin{description}
 
-\item[free-slip boundary condition (\np{rn\_shlat}\forcode{ = 0}):] the tangential velocity at
+\item [free-slip boundary condition ({\np[=0]{rn_shlat}{rn\_shlat}})] the tangential velocity at
   the coastline is equal to the offshore velocity,
   \ie\ the normal derivative of the tangential velocity is zero at the coast,
@@ -119 +123 @@
   (\autoref{fig:LBC_shlat}-a).
 
-\item[no-slip boundary condition (\np{rn\_shlat}\forcode{ = 2}):] the tangential velocity vanishes at the coastline.
+\item [no-slip boundary condition ({\np[=2]{rn_shlat}{rn\_shlat}})] the tangential velocity vanishes at the coastline.
   Assuming that the tangential velocity decreases linearly from
   the closest ocean velocity grid point to the coastline,
@@ -134 +138 @@
   the no-slip boundary condition, simply by multiplying it by the mask$_{f}$ :
   \[
-    % \label{eq:lbc_bbbb}
+    % \label{eq:LBC_bbbb}
     \zeta \equiv \frac{1}{e_{1f} {\kern 1pt}e_{2f} }\left( {\delta_{i+1/2}
         \left[ {e_{2v} \,v} \right]-\delta_{j+1/2} \left[ {e_{1u} \,u} \right]}
@@ -140 +144 @@
   \]
 
-\item["partial" free-slip boundary condition (0$<$\np{rn\_shlat}$<$2):] the tangential velocity at
+\item ["partial" free-slip boundary condition (0$<$\np{rn_shlat}{rn\_shlat}$<$2)] the tangential velocity at
   the coastline is smaller than the offshore velocity, \ie\ there is a lateral friction but
   not strong enough to make the tangential velocity at the coast vanish (\autoref{fig:LBC_shlat}-c).
   This can be selected by providing a value of mask$_{f}$ strictly inbetween $0$ and $2$.
 
-\item["strong" no-slip boundary condition (2$<$\np{rn\_shlat}):] the viscous boundary layer is assumed to
+\item ["strong" no-slip boundary condition (2$<$\np{rn_shlat}{rn\_shlat})] the viscous boundary layer is assumed to
   be smaller than half the grid size (\autoref{fig:LBC_shlat}-d).
   The friction is thus larger than in the no-slip case.
@@ -155 +159 @@
 it is only applied next to the coast where the minimum water depth can be quite shallow.
 
-
-% ================================================================
-% Boundary Condition around the Model Domain
-% ================================================================
-\section[Model domain boundary condition (\texttt{jperio})]
-{Model domain boundary condition (\protect\jp{jperio})}
+%% =================================================================================================
+\section[Model domain boundary condition (\forcode{jperio})]{Model domain boundary condition (\protect\jp{jperio})}
 \label{sec:LBC_jperio}
 
@@ -168 +168 @@
 The north-fold boundary condition is associated with the 3-pole ORCA mesh.
 
-% -------------------------------------------------------------------------------------------------------------
-%        Closed, cyclic (\jp{jperio}\forcode{ = 0..2})
-% -------------------------------------------------------------------------------------------------------------
-\subsection[Closed, cyclic (\forcode{jperio = [0127]})]
-{Closed, cyclic (\protect\jp{jperio}\forcode{ = [0127]})}
+%% =================================================================================================
+\subsection[Closed, cyclic (\forcode{=0,1,2,7})]{Closed, cyclic (\protect\jp{jperio}\forcode{=0,1,2,7})}
 \label{subsec:LBC_jperio012}
 
 The choice of closed or cyclic model domain boundary condition is made by
-setting \jp{jperio} to 0, 1, 2 or 7 in namelist \nam{cfg}.
+setting \jp{jperio} to 0, 1, 2 or 7 in namelist \nam{cfg}{cfg}.
 Each time such a boundary condition is needed, it is set by a call to routine \mdl{lbclnk}.
 The computation of momentum and tracer trends proceeds from $i=2$ to $i=jpi-1$ and from $j=2$ to $j=jpj-1$,
@@ -185 +182 @@
 \begin{description}
 
-\item[For closed boundary (\jp{jperio}\forcode{ = 0})],
-  solid walls are imposed at all model boundaries:
+\item [For closed boundary (\jp{jperio}\forcode{=0})], solid walls are imposed at all model boundaries:
   first and last rows and columns are set to zero.
 
-\item[For cyclic east-west boundary (\jp{jperio}\forcode{ = 1})],
-  first and last rows are set to zero (closed) whilst the first column is set to
+\item [For cyclic east-west boundary (\jp{jperio}\forcode{=1})], first and last rows are set to zero (closed) whilst the first column is set to
   the value of the last-but-one column and the last column to the value of the second one
   (\autoref{fig:LBC_jperio}-a).
   Whatever flows out of the eastern (western) end of the basin enters the western (eastern) end.
 
-\item[For cyclic north-south boundary (\jp{jperio}\forcode{ = 2})],
-  first and last columns are set to zero (closed) whilst the first row is set to
+\item [For cyclic north-south boundary (\jp{jperio}\forcode{=2})], first and last columns are set to zero (closed) whilst the first row is set to
   the value of the last-but-one row and the last row to the value of the second one
   (\autoref{fig:LBC_jperio}-a).
   Whatever flows out of the northern (southern) end of the basin enters the southern (northern) end.
 
-\item[Bi-cyclic east-west and north-south boundary (\jp{jperio}\forcode{ = 7})] combines cases 1 and 2.
+\item [Bi-cyclic east-west and north-south boundary (\jp{jperio}\forcode{=7})] combines cases 1 and 2.
 
 \end{description}
 
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_LBC_jperio}
-    \caption{
-      \protect\label{fig:LBC_jperio}
-      setting of (a) east-west cyclic  (b) symmetric across the equator boundary conditions.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=0.66\textwidth]{LBC_jperio}
+  \caption[Setting of east-west cyclic and symmetric across the Equator boundary conditions]{
+    Setting of (a) east-west cyclic (b) symmetric across the Equator boundary conditions}
+  \label{fig:LBC_jperio}
 \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-
-% -------------------------------------------------------------------------------------------------------------
-%        North fold (\textit{jperio = 3 }to $6)$
-% -------------------------------------------------------------------------------------------------------------
-\subsection[North-fold (\forcode{jperio = [3-6]})]
-{North-fold (\protect\jp{jperio}\forcode{ = [3-6]})}
+
+%% =================================================================================================
+\subsection[North-fold (\forcode{=3,6})]{North-fold (\protect\jp{jperio}\forcode{=3,6})}
 \label{subsec:LBC_north_fold}
 
 The north fold boundary condition has been introduced in order to handle the north boundary of
 a three-polar ORCA grid.
-Such a grid has two poles in the northern hemisphere (\autoref{fig:MISC_ORCA_msh},
-and thus requires a specific treatment illustrated in \autoref{fig:North_Fold_T}.
+Such a grid has two poles in the northern hemisphere (\autoref{fig:CFGS_ORCA_msh},
+and thus requires a specific treatment illustrated in \autoref{fig:LBC_North_Fold_T}.
 Further information can be found in \mdl{lbcnfd} module which applies the north fold boundary condition.
 
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_North_Fold_T}
-    \caption{
-      \protect\label{fig:North_Fold_T}
-      North fold boundary with a $T$-point pivot and cyclic east-west boundary condition ($jperio=4$),
-      as used in ORCA 2, 1/4, and 1/12.
-      Pink shaded area corresponds to the inner domain mask (see text).
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=0.66\textwidth]{LBC_North_Fold_T}
+  \caption[North fold boundary in ORCA 2\deg, 1/4\deg and 1/12\deg]{
+    North fold boundary with a $T$-point pivot and cyclic east-west boundary condition ($jperio=4$),
+    as used in ORCA 2\deg, 1/4\deg and 1/12\deg.
+    Pink shaded area corresponds to the inner domain mask (see text).}
+  \label{fig:LBC_North_Fold_T}
 \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-
-% ====================================================================
-% Exchange with neighbouring processors
-% ====================================================================
-\section[Exchange with neighbouring processors (\textit{lbclnk.F90}, \textit{lib\_mpp.F90})]
-{Exchange with neighbouring processors (\protect\mdl{lbclnk}, \protect\mdl{lib\_mpp})}
+
+%% =================================================================================================
+\section[Exchange with neighbouring processors (\textit{lbclnk.F90}, \textit{lib\_mpp.F90})]{Exchange with neighbouring processors (\protect\mdl{lbclnk}, \protect\mdl{lib\_mpp})}
 \label{sec:LBC_mpp}
 
+\begin{listing}
+  \nlst{nammpp}
+  \caption{\forcode{&nammpp}}
+  \label{lst:nammpp}
+\end{listing}
+
 For massively parallel processing (mpp), a domain decomposition method is used.
-The basic idea of the method is to split the large computation domain of a numerical experiment into
-several smaller domains and solve the set of equations by addressing independent local problems.
+The basic idea of the method is to split the large computation domain of a numerical experiment into several smaller domains and
+solve the set of equations by addressing independent local problems.
 Each processor has its own local memory and computes the model equation over a subdomain of the whole model domain.
-The subdomain boundary conditions are specified through communications between processors which
-are organized by explicit statements (message passing method).
-
-A big advantage is that the method does not need many modifications of the initial \fortran code.
-From the modeller's point of view, each sub domain running on a processor is identical to the "mono-domain" code.
-In addition, the programmer manages the communications between subdomains,
-and the code is faster when the number of processors is increased.
-The porting of OPA code on an iPSC860 was achieved during Guyon's PhD [Guyon et al. 1994, 1995]
-in collaboration with CETIIS and ONERA.
-The implementation in the operational context and the studies of performance on
-a T3D and T3E Cray computers have been made in collaboration with IDRIS and CNRS.
+The subdomain boundary conditions are specified through communications between processors which are organized by
+explicit statements (message passing method).
 The present implementation is largely inspired by Guyon's work [Guyon 1995].
 
@@ -272 +249 @@
 depend at the very most on one neighbouring point.
 The only non-local computations concern the vertical physics
-(implicit diffusion, turbulent closure scheme, ...) (delocalization over the whole water column),
-and the solving of the elliptic equation associated with the surface pressure gradient computation
-(delocalization over the whole horizontal domain).
+(implicit diffusion, turbulent closure scheme, ...).
 Therefore, a pencil strategy is used for the data sub-structuration:
 the 3D initial domain is laid out on local processor memories following a 2D horizontal topological splitting.
@@ -284 +259 @@
 each processor sends to its neighbouring processors the update values of the points corresponding to
 the interior overlapping area to its neighbouring sub-domain (\ie\ the innermost of the two overlapping rows).
-The communication is done through the Message Passing Interface (MPI).
+Communications are first done according to the east-west direction and next according to the north-south direction.
+There is no specific communications for the corners.
+The communication is done through the Message Passing Interface (MPI) and requires \key{mpp\_mpi}.
+Use also \key{mpi2} if MPI3 is not available on your computer.
 The data exchanges between processors are required at the very place where
 lateral domain boundary conditions are set in the mono-domain computation:
 the \rou{lbc\_lnk} routine (found in \mdl{lbclnk} module) which manages such conditions is interfaced with
-routines found in \mdl{lib\_mpp} module when running on an MPP computer (\ie\ when \key{mpp\_mpi} defined).
-It has to be pointed out that when using the MPP version of the model,
-the east-west cyclic boundary condition is done implicitly,
-whilst the south-symmetric boundary condition option is not available.
-
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+routines found in \mdl{lib\_mpp} module.
+The output file \textit{communication\_report.txt} provides the list of which routines do how
+many communications during 1 time step of the model.\\
+
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_mpp}
-    \caption{
-      \protect\label{fig:mpp}
-      Positioning of a sub-domain when massively parallel processing is used.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=0.66\textwidth]{LBC_mpp}
+  \caption{Positioning of a sub-domain when massively parallel processing is used}
+  \label{fig:LBC_mpp}
 \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-
-In the standard version of \NEMO, the splitting is regular and arithmetic.
-The i-axis is divided by \jp{jpni} and
-the j-axis by \jp{jpnj} for a number of processors \jp{jpnij} most often equal to $jpni \times jpnj$
-(parameters set in  \nam{mpp} namelist).
-Each processor is independent and without message passing or synchronous process,
-programs run alone and access just its own local memory.
-For this reason, the main model dimensions are now the local dimensions of the subdomain (pencil) that
-are named \jp{jpi}, \jp{jpj}, \jp{jpk}.
+
+In \NEMO, the splitting is regular and arithmetic.
+The total number of subdomains corresponds to the number of MPI processes allocated to \NEMO\ when the model is launched
+(\ie\ mpirun -np x ./nemo will automatically give x subdomains).
+The i-axis is divided by \np{jpni}{jpni} and the j-axis by \np{jpnj}{jpnj}.
+These parameters are defined in \nam{mpp}{mpp} namelist.
+If \np{jpni}{jpni} and \np{jpnj}{jpnj} are < 1, they will be automatically redefined in the code to give the best domain decomposition
+(see bellow).
+
+Each processor is independent and without message passing or synchronous process, programs run alone and access just its own local memory.
+For this reason,
+the main model dimensions are now the local dimensions of the subdomain (pencil) that are named \jp{jpi}, \jp{jpj}, \jp{jpk}.
 These dimensions include the internal domain and the overlapping rows.
-The number of rows to exchange (known as the halo) is usually set to one (\jp{jpreci}=1, in \mdl{par\_oce}).
+The number of rows to exchange (known as the halo) is usually set to one (nn\_hls=1, in \mdl{par\_oce},
+and must be kept to one until further notice).
 The whole domain dimensions are named \jp{jpiglo}, \jp{jpjglo} and \jp{jpk}.
 The relationship between the whole domain and a sub-domain is:
-\[
-  jpi = ( jpiglo-2*jpreci + (jpni-1) ) / jpni + 2*jpreci
-  jpj = ( jpjglo-2*jprecj + (jpnj-1) ) / jpnj + 2*jprecj
-\]
-where \jp{jpni}, \jp{jpnj} are the number of processors following the i- and j-axis.
-
-One also defines variables nldi and nlei which correspond to the internal domain bounds,
-and the variables nimpp and njmpp which are the position of the (1,1) grid-point in the global domain.
+\begin{gather*}
+  jpi = ( jpiglo-2\times nn\_hls + (jpni-1) ) / jpni + 2\times nn\_hls \\
+  jpj = ( jpjglo-2\times nn\_hls + (jpnj-1) ) / jpnj + 2\times nn\_hls
+\end{gather*}
+
+One also defines variables nldi and nlei which correspond to the internal domain bounds, and the variables nimpp and njmpp which are the position of the (1,1) grid-point in the global domain (\autoref{fig:LBC_mpp}). Note that since the version 4, there is no more extra-halo area as defined in \autoref{fig:LBC_mpp} so \jp{jpi} is now always equal to nlci and \jp{jpj} equal to nlcj.
+
 An element of $T_{l}$, a local array (subdomain) corresponds to an element of $T_{g}$,
 a global array (whole domain) by the relationship:
 \[
-  % \label{eq:lbc_nimpp}
+  % \label{eq:LBC_nimpp}
   T_{g} (i+nimpp-1,j+njmpp-1,k) = T_{l} (i,j,k),
 \]
-with  $1 \leq i \leq jpi$, $1  \leq j \leq jpj $ , and  $1  \leq k \leq jpk$.
-
-Processors are numbered from 0 to $jpnij-1$, the number is saved in the variable nproc.
-In the standard version, a processor has no more than
-four neighbouring processors named nono (for north), noea (east), noso (south) and nowe (west) and
-two variables, nbondi and nbondj, indicate the relative position of the processor:
-\begin{itemize}
-\item       nbondi = -1    an east neighbour, no west processor,
-\item       nbondi =  0 an east neighbour, a west neighbour,
-\item       nbondi =  1    no east processor, a west neighbour,
-\item       nbondi =  2    no splitting following the i-axis.
-\end{itemize}
-During the simulation, processors exchange data with their neighbours.
-If there is effectively a neighbour, the processor receives variables from this processor on its overlapping row,
-and sends the data issued from internal domain corresponding to the overlapping row of the other processor.
-
-
-The \NEMO\ model computes equation terms with the help of mask arrays (0 on land points and 1 on sea points).
-It is easily readable and very efficient in the context of a computer with vectorial architecture.
-However, in the case of a scalar processor, computations over the land regions become more expensive in
-terms of CPU time.
-It is worse when we use a complex configuration with a realistic bathymetry like the global ocean where
-more than 50 \% of points are land points.
-For this reason, a pre-processing tool can be used to choose the mpp domain decomposition with a maximum number of
-only land points processors, which can then be eliminated (\autoref{fig:mppini2})
-(For example, the mpp\_optimiz tools, available from the DRAKKAR web site).
-This optimisation is dependent on the specific bathymetry employed.
-The user then chooses optimal parameters \jp{jpni}, \jp{jpnj} and \jp{jpnij} with $jpnij < jpni \times jpnj$,
-leading to the elimination of $jpni \times jpnj - jpnij$ land processors.
-When those parameters are specified in \nam{mpp} namelist,
-the algorithm in the \rou{inimpp2} routine sets each processor's parameters (nbound, nono, noea,...) so that
-the land-only processors are not taken into account.
-
-\gmcomment{Note that the inimpp2 routine is general so that the original inimpp
-routine should be suppressed from the code.}
-
-When land processors are eliminated,
-the value corresponding to these locations in the model output files is undefined.
-Note that this is a problem for the meshmask file which requires to be defined over the whole domain.
-Therefore, user should not eliminate land processors when creating a meshmask file
-(\ie\ when setting a non-zero value to \np{nn\_msh}).
-
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+with $1 \leq i \leq jpi$, $1  \leq j \leq jpj $ , and  $1  \leq k \leq jpk$.
+
+The 1-d arrays $mig(1:\jp{jpi})$ and $mjg(1:\jp{jpj})$, defined in \rou{dom\_glo} routine (\mdl{domain} module), should be used to get global domain indices from local domain indices. The 1-d arrays, $mi0(1:\jp{jpiglo})$, $mi1(1:\jp{jpiglo})$ and $mj0(1:\jp{jpjglo})$, $mj1(1:\jp{jpjglo})$ have the reverse purpose and should be used to define loop indices expressed in global domain indices (see examples in \mdl{dtastd} module).\\
+
+The \NEMO\ model computes equation terms with the help of mask arrays (0 on land points and 1 on sea points). It is therefore possible that an MPI subdomain contains only land points. To save ressources, we try to supress from the computational domain as much land subdomains as possible. For example if $N_{mpi}$ processes are allocated to NEMO, the domain decomposition will be given by the following equation:
+\[
+  N_{mpi} = jpni \times jpnj - N_{land} + N_{useless}
+\]
+$N_{land}$ is the total number of land subdomains in the domain decomposition defined by \np{jpni}{jpni} and \np{jpnj}{jpnj}. $N_{useless}$ is the number of land subdomains that are kept in the compuational domain in order to make sure that $N_{mpi}$ MPI processes are indeed allocated to a given subdomain. The values of $N_{mpi}$, \np{jpni}{jpni}, \np{jpnj}{jpnj},  $N_{land}$ and $N_{useless}$ are printed in the output file \texttt{ocean.output}. $N_{useless}$ must, of course, be as small as possible to limit the waste of ressources. A warning is issued in  \texttt{ocean.output} if $N_{useless}$ is not zero. Note that non-zero value of $N_{useless}$ is uselly required when using AGRIF as, up to now, the parent grid and each of the child grids must use all the $N_{mpi}$ processes.
+
+If the domain decomposition is automatically defined (when \np{jpni}{jpni} and \np{jpnj}{jpnj} are < 1), the decomposition chosen by the model will minimise the sub-domain size (defined as $max_{all domains}(jpi \times jpj)$) and maximize the number of eliminated land subdomains. This means that no other domain decomposition (a set of \np{jpni}{jpni} and \np{jpnj}{jpnj} values) will use less processes than $(jpni  \times  jpnj - N_{land})$ and get a smaller subdomain size.
+In order to specify $N_{mpi}$ properly (minimize $N_{useless}$), you must run the model once with \np{ln_list}{ln\_list} activated. In this case, the model will start the initialisation phase, print the list of optimum decompositions ($N_{mpi}$, \np{jpni}{jpni} and \np{jpnj}{jpnj}) in \texttt{ocean.output} and directly abort. The maximum value of $N_{mpi}$ tested in this list is given by $max(N_{MPI\_tasks}, jpni \times jpnj)$. For example, run the model on 40 nodes with ln\_list activated and $jpni = 10000$ and $jpnj = 1$, will print the list of optimum domains decomposition from 1 to about 10000.
+
+Processors are numbered from 0 to $N_{mpi} - 1$. Subdomains containning some ocean points are numbered first from 0 to $jpni * jpnj - N_{land} -1$. The remaining $N_{useless}$ land subdomains are numbered next, which means that, for a given (\np{jpni}{jpni}, \np{jpnj}{jpnj}), the numbers attributed to he ocean subdomains do not vary with $N_{useless}$.
+
+When land processors are eliminated, the value corresponding to these locations in the model output files is undefined. \np{ln_mskland}{ln\_mskland} must be activated in order avoid Not a Number values in output files. Note that it is better to not eliminate land processors when creating a meshmask file (\ie\ when setting a non-zero value to \np{nn_msh}{nn\_msh}).
+
 \begin{figure}[!ht]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_mppini2}
-    \caption {
-      \protect\label{fig:mppini2}
-      Example of Atlantic domain defined for the CLIPPER projet.
-      Initial grid is composed of 773 x 1236 horizontal points.
-      (a) the domain is split onto 9 \time 20 subdomains (jpni=9, jpnj=20).
-      52 subdomains are land areas.
-      (b) 52 subdomains are eliminated (white rectangles) and
-      the resulting number of processors really used during the computation is jpnij=128.
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=0.66\textwidth]{LBC_mppini2}
+  \caption[Atlantic domain defined for the CLIPPER projet]{
+    Example of Atlantic domain defined for the CLIPPER projet.
+    Initial grid is composed of 773 x 1236 horizontal points.
+    (a) the domain is split onto 9 $times$ 20 subdomains (jpni=9, jpnj=20).
+    52 subdomains are land areas.
+    (b) 52 subdomains are eliminated (white rectangles) and
+    the resulting number of processors really used during the computation is jpnij=128.}
+  \label{fig:LBC_mppini2}
 \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-
-
-% ====================================================================
-% Unstructured open boundaries BDY
-% ====================================================================
+
+%% =================================================================================================
 \section{Unstructured open boundary conditions (BDY)}
 \label{sec:LBC_bdy}
 
-%-----------------------------------------nambdy--------------------------------------------
-
-\nlst{nambdy}
-%-----------------------------------------------------------------------------------------------
-%-----------------------------------------nambdy_dta--------------------------------------------
-
-\nlst{nambdy_dta}
-%-----------------------------------------------------------------------------------------------
-
-Options are defined through the \nam{bdy} \nam{bdy\_dta} namelist variables.
+\begin{listing}
+  \nlst{nambdy}
+  \caption{\forcode{&nambdy}}
+  \label{lst:nambdy}
+\end{listing}
+
+\begin{listing}
+  \nlst{nambdy_dta}
+  \caption{\forcode{&nambdy_dta}}
+  \label{lst:nambdy_dta}
+\end{listing}
+
+Options are defined through the \nam{bdy}{bdy} and \nam{bdy_dta}{bdy\_dta} namelist variables.
 The BDY module is the core implementation of open boundary conditions for regional configurations on
-temperature, salinity, barotropic and baroclinic velocities, as well as ice concentration, ice and snow thicknesses.
+ocean temperature, salinity, barotropic-baroclinic velocities, ice-snow concentration, thicknesses, temperatures, salinity and melt ponds concentration and thickness.
 
 The BDY module was modelled on the OBC module (see \NEMO\ 3.4) and shares many features and
@@ -417 +363 @@
 See the section on the Input Boundary Data Files for details.
 
-%----------------------------------------------
+%% =================================================================================================
 \subsection{Namelists}
-\label{subsec:BDY_namelist}
-
-The BDY module is activated by setting \np{ln\_bdy}\forcode{ = .true.} .
+\label{subsec:LBC_bdy_namelist}
+
+The BDY module is activated by setting \np[=.true.]{ln_bdy}{ln\_bdy} .
 It is possible to define more than one boundary ``set'' and apply different boundary conditions to each set.
-The number of boundary sets is defined by \np{nb\_bdy}.
-Each boundary set may be defined as a set of straight line segments in a namelist
-(\np{ln\_coords\_file}\forcode{ = .false.}) or read in from a file (\np{ln\_coords\_file}\forcode{ = .true.}).
-If the set is defined in a namelist, then the namelists \nam{bdy\_index} must be included separately, one for each set.
-If the set is defined by a file, then a ``\ifile{coordinates.bdy}'' file must be provided.
+The number of boundary sets is defined by \np{nb_bdy}{nb\_bdy}.
+Each boundary set can be either defined as a series of straight line segments directly in the namelist
+(\np[=.false.]{ln_coords_file}{ln\_coords\_file}, and a namelist block \nam{bdy_index}{bdy\_index} must be included for each set) or read in from a file (\np[=.true.]{ln_coords_file}{ln\_coords\_file}, and a ``\ifile{coordinates.bdy}'' file must be provided).
 The coordinates.bdy file is analagous to the usual \NEMO\ ``\ifile{coordinates}'' file.
 In the example above, there are two boundary sets, the first of which is defined via a file and
-the second is defined in a namelist.
-For more details of the definition of the boundary geometry see section \autoref{subsec:BDY_geometry}.
+the second is defined in the namelist.
+For more details of the definition of the boundary geometry see section \autoref{subsec:LBC_bdy_geometry}.
 
 For each boundary set a boundary condition has to be chosen for the barotropic solution
 (``u2d'':sea-surface height and barotropic velocities), for the baroclinic velocities (``u3d''),
-for the active tracers \footnote{The BDY module does not deal with passive tracers at this version} (``tra''), and sea-ice (``ice'').
-For each set of variables there is a choice of algorithm and a choice for the data,
-eg. for the active tracers the algorithm is set by \np{cn\_tra} and the choice of data is set by \np{nn\_tra\_dta}.\\
+for the active tracers \footnote{The BDY module does not deal with passive tracers at this version} (``tra''), and for sea-ice (``ice'').
+For each set of variables one has to choose an algorithm and the boundary data (set resp. by \np{cn_tra}{cn\_tra} and \np{nn_tra_dta}{nn\_tra\_dta} for tracers).\\
 
 The choice of algorithm is currently as follows:
 
 \begin{description}
-\item[\forcode{'none'}:] No boundary condition applied.
+\item [\forcode{'none'}:] No boundary condition applied.
   So the solution will ``see'' the land points around the edge of the edge of the domain.
-\item[\forcode{'specified'}:] Specified boundary condition applied (only available for baroclinic velocity and tracer variables).
-\item[\forcode{'neumann'}:] Value at the boundary are duplicated (No gradient). Only available for baroclinic velocity and tracer variables.
-\item[\forcode{'frs'}:] Flow Relaxation Scheme (FRS) available for all variables.
-\item[\forcode{'Orlanski'}:] Orlanski radiation scheme (fully oblique) for barotropic, baroclinic and tracer variables.
-\item[\forcode{'Orlanski_npo'}:] Orlanski radiation scheme for barotropic, baroclinic and tracer variables.
-\item[\forcode{'flather'}:] Flather radiation scheme for the barotropic variables only.
+\item [\forcode{'specified'}:] Specified boundary condition applied (only available for baroclinic velocity and tracer variables).
+\item [\forcode{'neumann'}:] Value at the boundary are duplicated (No gradient). Only available for baroclinic velocity and tracer variables.
+\item [\forcode{'frs'}:] Flow Relaxation Scheme (FRS) available for all variables.
+\item [\forcode{'Orlanski'}:] Orlanski radiation scheme (fully oblique) for barotropic, baroclinic and tracer variables.
+\item [\forcode{'Orlanski_npo'}:] Orlanski radiation scheme for barotropic, baroclinic and tracer variables.
+\item [\forcode{'flather'}:] Flather radiation scheme for the barotropic variables only.
 \end{description}
 
-The main choice for the boundary data is to use initial conditions as boundary data
-(\np{nn\_tra\_dta}\forcode{ = 0}) or to use external data from a file (\np{nn\_tra\_dta}\forcode{ = 1}).
+The boundary data is either set to initial conditions
+(\np[=0]{nn_tra_dta}{nn\_tra\_dta}) or forced with external data from a file (\np[=1]{nn_tra_dta}{nn\_tra\_dta}).
 In case the 3d velocity data contain the total velocity (ie, baroclinic and barotropic velocity),
-the bdy code can derived baroclinic and barotropic velocities by setting \np{ln\_full\_vel}\forcode{ = .true. }
+the bdy code can derived baroclinic and barotropic velocities by setting \np[=.true.]{ln_full_vel}{ln\_full\_vel}
 For the barotropic solution there is also the option to use tidal harmonic forcing either by
-itself (\np{nn\_dyn2d\_dta}\forcode{ = 2}) or in addition to other external data (\np{nn\_dyn2d\_dta}\forcode{ = 3}).\\
-Sea-ice salinity, temperature and age data at the boundary are constant and defined repectively by \np{rn\_ice\_sal}, \np{rn\_ice\_tem} and \np{rn\_ice\_age}.
-
-If external boundary data is required then the \nam{bdy\_dta} namelist must be defined.
-One \nam{bdy\_dta} namelist is required for each boundary set, adopting the same order of indexes in which the boundary sets are defined in nambdy.
-In the example given, two boundary sets have been defined. The first one is reading data file in the \nam{bdy\_dta} namelist shown above
+itself (\np[=2]{nn_dyn2d_dta}{nn\_dyn2d\_dta}) or in addition to other external data (\np[=3]{nn_dyn2d_dta}{nn\_dyn2d\_dta}).\\
+If not set to initial conditions, sea-ice salinity, temperatures and melt ponds data at the boundary can either be read in a file or defined as constant (by \np{rn_ice_sal}{rn\_ice\_sal}, \np{rn_ice_tem}{rn\_ice\_tem}, \np{rn_ice_apnd}{rn\_ice\_apnd}, \np{rn_ice_hpnd}{rn\_ice\_hpnd}). Ice age is constant and defined by \np{rn_ice_age}{rn\_ice\_age}.
+
+If external boundary data is required then the \nam{bdy_dta}{bdy\_dta} namelist must be defined.
+One \nam{bdy_dta}{bdy\_dta} namelist is required for each boundary set, adopting the same order of indexes in which the boundary sets are defined in nambdy.
+In the example given, two boundary sets have been defined. The first one is reading data file in the \nam{bdy_dta}{bdy\_dta} namelist shown above
 and the second one is using data from intial condition (no namelist block needed).
 The boundary data is read in using the fldread module,
-so the \nam{bdy\_dta} namelist is in the format required for fldread.
+so the \nam{bdy_dta}{bdy\_dta} namelist is in the format required for fldread.
 For each required variable, the filename, the frequency of the files and
 the frequency of the data in the files are given.
-Also whether or not time-interpolation is required and whether the data is climatological (time-cyclic) data.\\
+Also whether or not time-interpolation is required and whether the data is climatological (time-cyclic) data.
+For sea-ice salinity, temperatures and melt ponds, reading the files are skipped and constant values are used if filenames are defined as {'NOT USED'}.\\
 
 There is currently an option to vertically interpolate the open boundary data onto the native grid at run-time.
-If \np{nn\_bdy\_jpk} $< -1$, it is assumed that the lateral boundary data are already on the native grid.
-However, if \np{nn\_bdy\_jpk} is set to the number of vertical levels present in the boundary data,
+If \np{nn_bdy_jpk}{nn\_bdy\_jpk}$<-1$, it is assumed that the lateral boundary data are already on the native grid.
+However, if \np{nn_bdy_jpk}{nn\_bdy\_jpk} is set to the number of vertical levels present in the boundary data,
 a bilinear interpolation onto the native grid will be triggered at runtime.
 For this to be successful the additional variables: $gdept$, $gdepu$, $gdepv$, $e3t$, $e3u$ and $e3v$, are required to be present in the lateral boundary files.
@@ -486 +430 @@
 FRS conditions are applied on temperature and salinity and climatological data is read from initial condition files.
 
-%----------------------------------------------
+%% =================================================================================================
 \subsection{Flow relaxation scheme}
-\label{subsec:BDY_FRS_scheme}
+\label{subsec:LBC_bdy_FRS_scheme}
 
 The Flow Relaxation Scheme (FRS) \citep{davies_QJRMS76,engedahl_T95},
@@ -495 +439 @@
 Given a model prognostic variable $\Phi$
 \[
-  % \label{eq:bdy_frs1}
+  % \label{eq:LBC_bdy_frs1}
   \Phi(d) = \alpha(d)\Phi_{e}(d) + (1-\alpha(d))\Phi_{m}(d)\;\;\;\;\; d=1,N
 \]
@@ -504 +448 @@
 the prognostic equation for $\Phi$ of the form:
 \[
-  % \label{eq:bdy_frs2}
+  % \label{eq:LBC_bdy_frs2}
   -\frac{1}{\tau}\left(\Phi - \Phi_{e}\right)
 \]
 where the relaxation time scale $\tau$ is given by a function of $\alpha$ and the model time step $\Delta t$:
 \[
-  % \label{eq:bdy_frs3}
+  % \label{eq:LBC_bdy_frs3}
   \tau = \frac{1-\alpha}{\alpha}  \,\rdt
 \]
@@ -519 +463 @@
 The function $\alpha$ is specified as a $tanh$ function:
 \[
-  % \label{eq:bdy_frs4}
+  % \label{eq:LBC_bdy_frs4}
   \alpha(d) = 1 - \tanh\left(\frac{d-1}{2}\right),       \quad d=1,N
 \]
-The width of the FRS zone is specified in the namelist as \np{nn\_rimwidth}.
+The width of the FRS zone is specified in the namelist as \np{nn_rimwidth}{nn\_rimwidth}.
 This is typically set to a value between 8 and 10.
 
-%----------------------------------------------
+%% =================================================================================================
 \subsection{Flather radiation scheme}
-\label{subsec:BDY_flather_scheme}
+\label{subsec:LBC_bdy_flather_scheme}
 
 The \citet{flather_JPO94} scheme is a radiation condition on the normal,
 depth-mean transport across the open boundary.
 It takes the form
-\begin{equation}  \label{eq:bdy_fla1}
-U = U_{e} + \frac{c}{h}\left(\eta - \eta_{e}\right),
+\begin{equation}
+  \label{eq:LBC_bdy_fla1}
+  U = U_{e} + \frac{c}{h}\left(\eta - \eta_{e}\right),
 \end{equation}
 where $U$ is the depth-mean velocity normal to the boundary and $\eta$ is the sea surface height,
@@ -542 +487 @@
 the external depth-mean normal velocity,
 plus a correction term that allows gravity waves generated internally to exit the model boundary.
-Note that the sea-surface height gradient in \autoref{eq:bdy_fla1} is a spatial gradient across the model boundary,
+Note that the sea-surface height gradient in \autoref{eq:LBC_bdy_fla1} is a spatial gradient across the model boundary,
 so that $\eta_{e}$ is defined on the $T$ points with $nbr=1$ and $\eta$ is defined on the $T$ points with $nbr=2$.
 $U$ and $U_{e}$ are defined on the $U$ or $V$ points with $nbr=1$, \ie\ between the two $T$ grid points.
 
-%----------------------------------------------
+%% =================================================================================================
 \subsection{Orlanski radiation scheme}
-\label{subsec:BDY_orlanski_scheme}
+\label{subsec:LBC_bdy_orlanski_scheme}
 
 The Orlanski scheme is based on the algorithm described by \citep{marchesiello.mcwilliams.ea_OM01}, hereafter MMS.
@@ -554 +499 @@
 The adaptive Orlanski condition solves a wave plus relaxation equation at the boundary:
 \begin{equation}
-\frac{\partial\phi}{\partial t} + c_x \frac{\partial\phi}{\partial x} + c_y \frac{\partial\phi}{\partial y} =
-                                                -\frac{1}{\tau}(\phi - \phi^{ext})
-\label{eq:wave_continuous}
+  \label{eq:LBC_wave_continuous}
+  \frac{\partial\phi}{\partial t} + c_x \frac{\partial\phi}{\partial x} + c_y \frac{\partial\phi}{\partial y} =
+  -\frac{1}{\tau}(\phi - \phi^{ext})
 \end{equation}
 
@@ -562 +507 @@
 velocities are diagnosed from the model fields as:
 
-\begin{equation} \label{eq:cx}
-c_x = -\frac{\partial\phi}{\partial t}\frac{\partial\phi / \partial x}{(\partial\phi /\partial x)^2 + (\partial\phi /\partial y)^2}
+\begin{equation}
+  \label{eq:LBC_cx}
+  c_x = -\frac{\partial\phi}{\partial t}\frac{\partial\phi / \partial x}{(\partial\phi /\partial x)^2 + (\partial\phi /\partial y)^2}
 \end{equation}
 \begin{equation}
-\label{eq:cy}
-c_y = -\frac{\partial\phi}{\partial t}\frac{\partial\phi / \partial y}{(\partial\phi /\partial x)^2 + (\partial\phi /\partial y)^2}
+  \label{eq:LBC_cy}
+  c_y = -\frac{\partial\phi}{\partial t}\frac{\partial\phi / \partial y}{(\partial\phi /\partial x)^2 + (\partial\phi /\partial y)^2}
 \end{equation}
 
 (As noted by MMS, this is a circular diagnosis of the phase speeds which only makes sense on a discrete grid).
-Equation (\autoref{eq:wave_continuous}) is defined adaptively depending on the sign of the phase velocity normal to the boundary $c_x$.
+Equation (\autoref{eq:LBC_wave_continuous}) is defined adaptively depending on the sign of the phase velocity normal to the boundary $c_x$.
 For $c_x$ outward, we have
 
@@ -581 +527 @@
 
 \begin{equation}
-\tau = \tau_{in}\,\,\,;\,\,\, c_x = c_y = 0
-\label{eq:tau_in}
+  \label{eq:LBC_tau_in}
+  \tau = \tau_{in}\,\,\,;\,\,\, c_x = c_y = 0
 \end{equation}
 
-Generally the relaxation time scale at inward propagation points (\np{rn\_time\_dmp}) is set much shorter than the time scale at outward propagation
-points (\np{rn\_time\_dmp\_out}) so that the solution is constrained more strongly by the external data at inward propagation points.
-See \autoref{subsec:BDY_relaxation} for detailed on the spatial shape of the scaling.\\
+Generally the relaxation time scale at inward propagation points (\np{rn_time_dmp}{rn\_time\_dmp}) is set much shorter than the time scale at outward propagation
+points (\np{rn_time_dmp_out}{rn\_time\_dmp\_out}) so that the solution is constrained more strongly by the external data at inward propagation points.
+See \autoref{subsec:LBC_bdy_relaxation} for detailed on the spatial shape of the scaling.\\
 The ``normal propagation of oblique radiation'' or NPO approximation (called \forcode{'orlanski_npo'}) involves assuming
-that $c_y$ is zero in equation (\autoref{eq:wave_continuous}), but including
-this term in the denominator of equation (\autoref{eq:cx}). Both versions of the scheme are options in BDY. Equations
-(\autoref{eq:wave_continuous}) - (\autoref{eq:tau_in}) correspond to equations (13) - (15) and (2) - (3) in MMS.\\
-
-%----------------------------------------------
+that $c_y$ is zero in equation (\autoref{eq:LBC_wave_continuous}), but including
+this term in the denominator of equation (\autoref{eq:LBC_cx}). Both versions of the scheme are options in BDY. Equations
+(\autoref{eq:LBC_wave_continuous}) - (\autoref{eq:LBC_tau_in}) correspond to equations (13) - (15) and (2) - (3) in MMS.\\
+
+%% =================================================================================================
 \subsection{Relaxation at the boundary}
-\label{subsec:BDY_relaxation}
-
-In addition to a specific boundary condition specified as \np{cn\_tra} and \np{cn\_dyn3d}, relaxation on baroclinic velocities and tracers variables are available.
-It is control by the namelist parameter \np{ln\_tra\_dmp} and \np{ln\_dyn3d\_dmp} for each boundary set.
-
-The relaxation time scale value (\np{rn\_time\_dmp} and \np{rn\_time\_dmp\_out}, $\tau$) are defined at the boundaries itself.
-This time scale ($\alpha$) is weighted by the distance ($d$) from the boundary over \np{nn\_rimwidth} cells ($N$):
+\label{subsec:LBC_bdy_relaxation}
+
+In addition to a specific boundary condition specified as \np{cn_tra}{cn\_tra} and \np{cn_dyn3d}{cn\_dyn3d}, relaxation on baroclinic velocities and tracers variables are available.
+It is control by the namelist parameter \np{ln_tra_dmp}{ln\_tra\_dmp} and \np{ln_dyn3d_dmp}{ln\_dyn3d\_dmp} for each boundary set.
+
+The relaxation time scale value (\np{rn_time_dmp}{rn\_time\_dmp} and \np{rn_time_dmp_out}{rn\_time\_dmp\_out}, $\tau$) are defined at the boundaries itself.
+This time scale ($\alpha$) is weighted by the distance ($d$) from the boundary over \np{nn_rimwidth}{nn\_rimwidth} cells ($N$):
 
 \[
@@ -609 +555 @@
 The same scaling is applied in the Orlanski damping.
 
-%----------------------------------------------
+%% =================================================================================================
 \subsection{Boundary geometry}
-\label{subsec:BDY_geometry}
+\label{subsec:LBC_bdy_geometry}
 
 Each open boundary set is defined as a list of points.
@@ -620 +566 @@
 the boundary point is increasingly further away from the edge of the model domain.
 A set of $nbi$, $nbj$, and $nbr$ arrays is defined for each of the $T$, $U$ and $V$ grids.
-Figure \autoref{fig:LBC_bdy_geom} shows an example of an irregular boundary.
+\autoref{fig:LBC_bdy_geom} shows an example of an irregular boundary.
 
 The boundary geometry for each set may be defined in a namelist nambdy\_index or
@@ -630 +576 @@
 \jp{jpinft} give the start and end $i$ indices for each segment with similar for the other boundaries.
 These segments define a list of $T$ grid points along the outermost row of the boundary ($nbr\,=\, 1$).
-The code deduces the $U$ and $V$ points and also the points for $nbr\,>\, 1$ if \np{nn\_rimwidth}\forcode{ > 1}.
+The code deduces the $U$ and $V$ points and also the points for $nbr\,>\, 1$ if \np[>1]{nn_rimwidth}{nn\_rimwidth}.
 
 The boundary geometry may also be defined from a ``\ifile{coordinates.bdy}'' file.
-Figure \autoref{fig:LBC_nc_header} gives an example of the header information from such a file, based on the description of geometrical setup given above.
+\autoref{fig:LBC_nc_header} gives an example of the header information from such a file, based on the description of geometrical setup given above.
 The file should contain the index arrays for each of the $T$, $U$ and $V$ grids.
 The arrays must be in order of increasing $nbr$.
@@ -645 +591 @@
 For example, if an open boundary is defined along an isobath, say at the shelf break,
 then the areas of ocean outside of this boundary will need to be masked out.
-This can be done by reading a mask file defined as \np{cn\_mask\_file} in the nam\_bdy namelist.
+This can be done by reading a mask file defined as \np{cn_mask_file}{cn\_mask\_file} in the nam\_bdy namelist.
 Only one mask file is used even if multiple boundary sets are defined.
 
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_LBC_bdy_geom}
-    \caption {
-      \protect\label{fig:LBC_bdy_geom}
-      Example of geometry of unstructured open boundary
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=0.66\textwidth]{LBC_bdy_geom}
+  \caption[Geometry of unstructured open boundary]{Example of geometry of unstructured open boundary}
+  \label{fig:LBC_bdy_geom}
 \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-
-%----------------------------------------------
+
+%% =================================================================================================
 \subsection{Input boundary data files}
-\label{subsec:BDY_data}
+\label{subsec:LBC_bdy_data}
 
 The data files contain the data arrays in the order in which the points are defined in the $nbi$ and $nbj$ arrays.
@@ -685 +626 @@
 These restrictions mean that data files used with versions of the
 model prior to Version 3.4 may not work with Version 3.4 onwards.
-A \fortran utility {\itshape bdy\_reorder} exists in the TOOLS directory which
+A \fortran\ utility {\itshape bdy\_reorder} exists in the TOOLS directory which
 will re-order the data in old BDY data files.
 
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[!t]
-  \begin{center}
-    \includegraphics[width=\textwidth]{Fig_LBC_nc_header}
-    \caption {
-      \protect\label{fig:LBC_nc_header}
-      Example of the header for a \protect\ifile{coordinates.bdy} file
-    }
-  \end{center}
+  \centering
+  \includegraphics[width=0.66\textwidth]{LBC_nc_header}
+  \caption[Header for a \protect\ifile{coordinates.bdy} file]{
+    Example of the header for a \protect\ifile{coordinates.bdy} file}
+  \label{fig:LBC_nc_header}
 \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-
-%----------------------------------------------
+
+%% =================================================================================================
 \subsection{Volume correction}
-\label{subsec:BDY_vol_corr}
+\label{subsec:LBC_bdy_vol_corr}
 
 There is an option to force the total volume in the regional model to be constant.
-This is controlled  by the \np{ln\_vol} parameter in the namelist.
-A value of \np{ln\_vol}\forcode{ = .false.} indicates that this option is not used.
-Two options to control the volume are available (\np{nn\_volctl}).
-If \np{nn\_volctl}\forcode{ = 0} then a correction is applied to the normal barotropic velocities around the boundary at
+This is controlled  by the \np{ln_vol}{ln\_vol} parameter in the namelist.
+A value of \np[=.false.]{ln_vol}{ln\_vol} indicates that this option is not used.
+Two options to control the volume are available (\np{nn_volctl}{nn\_volctl}).
+If \np[=0]{nn_volctl}{nn\_volctl} then a correction is applied to the normal barotropic velocities around the boundary at
 each timestep to ensure that the integrated volume flow through the boundary is zero.
-If \np{nn\_volctl}\forcode{ = 1} then the calculation of the volume change on
+If \np[=1]{nn_volctl}{nn\_volctl} then the calculation of the volume change on
 the timestep includes the change due to the freshwater flux across the surface and
 the correction velocity corrects for this as well.
@@ -717 +654 @@
 applied to all boundaries at once.
 
-%----------------------------------------------
+%% =================================================================================================
 \subsection{Tidal harmonic forcing}
-\label{subsec:BDY_tides}
-
-%-----------------------------------------nambdy_tide--------------------------------------------
-
-\nlst{nambdy_tide}
-%-----------------------------------------------------------------------------------------------
+\label{subsec:LBC_bdy_tides}
+
+\begin{listing}
+  \nlst{nambdy_tide}
+  \caption{\forcode{&nambdy_tide}}
+  \label{lst:nambdy_tide}
+\end{listing}
 
 Tidal forcing at open boundaries requires the activation of surface
-tides (i.e., in \nam{\_tide}, \np{ln\_tide} needs to be set to
+tides (i.e., in \nam{_tide}{\_tide}, \np{ln_tide}{ln\_tide} needs to be set to
 \forcode{.true.} and the required constituents need to be activated by
-including their names in the \np{clname} array; see
+including their names in the \np{clname}{clname} array; see
 \autoref{sec:SBC_tide}). Specific options related to the reading in of
 the complex harmonic amplitudes of elevation (SSH) and barotropic
 velocity (u,v) at open boundaries are defined through the
-\nam{bdy\_tide} namelist parameters.\\
+\nam{bdy_tide}{bdy\_tide} namelist parameters.\\
 
 The tidal harmonic data at open boundaries can be specified in two
 different ways, either on a two-dimensional grid covering the entire
 model domain or along open boundary segments; these two variants can
-be selected by setting \np{ln\_bdytide\_2ddta } to \forcode{.true.} or
+be selected by setting \np{ln_bdytide_2ddta }{ln\_bdytide\_2ddta } to \forcode{.true.} or
 \forcode{.false.}, respectively. In either case, the real and
 imaginary parts of SSH and the two barotropic velocity components for
@@ -744 +682 @@
 separately: when two-dimensional data is used, variables
 \textit{tcname\_z1} and \textit{tcname\_z2} for real and imaginary SSH,
-respectively, are expected in input file \np{filtide} with suffix
+respectively, are expected in input file \np{filtide}{filtide} with suffix
 \ifile{\_grid\_T}, variables \textit{tcname\_u1} and
 \textit{tcname\_u2} for real and imaginary u, respectively, are
-expected in input file \np{filtide} with suffix \ifile{\_grid\_U}, and
+expected in input file \np{filtide}{filtide} with suffix \ifile{\_grid\_U}, and
 \textit{tcname\_v1} and \textit{tcname\_v2} for real and imaginary v,
-respectively, are expected in input file \np{filtide} with suffix
+respectively, are expected in input file \np{filtide}{filtide} with suffix
 \ifile{\_grid\_V}; when data along open boundary segments is used,
 variables \textit{z1} and \textit{z2} (real and imaginary part of SSH)
-are expected to be available from file \np{filtide} with suffix
+are expected to be available from file \np{filtide}{filtide} with suffix
 \ifile{tcname\_grid\_T}, variables \textit{u1} and \textit{u2} (real
 and imaginary part of u) are expected to be available from file
-\np{filtide} with suffix \ifile{tcname\_grid\_U}, and variables
+\np{filtide}{filtide} with suffix \ifile{tcname\_grid\_U}, and variables
 \textit{v1} and \textit{v2} (real and imaginary part of v) are
-expected to be available from file \np{filtide} with suffix
-\ifile{tcname\_grid\_V}. If \np{ln\_bdytide\_conj} is set to
+expected to be available from file \np{filtide}{filtide} with suffix
+\ifile{tcname\_grid\_V}. If \np{ln_bdytide_conj}{ln\_bdytide\_conj} is set to
 \forcode{.true.}, the data is expected to be in complex conjugate
 form.
@@ -770 +708 @@
 direction of rotation). %, e.g. anticlockwise or clockwise.
 
-\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-*