Changeset 14644 for NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/NEMO/subfiles/chap_LBC.tex

Timestamp:

2021-03-26T15:33:49+01:00 (3 years ago)

Author:

sparonuz

Message:

Merge trunk -r14642:HEAD

Location:

NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final

Files:

• . (modified) (1 prop)
• doc/latex/NEMO/subfiles (modified) (1 prop)
• doc/latex/NEMO/subfiles/chap_LBC.tex (modified) (13 diffs)

NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final

@@ -9 +9 @@
 
 # SETTE
-^/utils/CI/sette_wave@13990         sette
+^/utils/CI/sette@14244        sette

@@ -9 +9 @@
 
 # SETTE
-^/utils/CI/sette_wave@13990         sette
+^/utils/CI/sette@14244        sette

NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/NEMO/subfiles

@@ +1 @@
+*.aux
+*.bbl
+*.blg
+*.fdb*
+*.fls
+*.idx
+*.ilg
 *.ind
-*.ilg
+*.lo*
+*.out
+*.pdf
+*.pyg
+*.tdo
+*.toc
+*.xdv
+cache*

@@ +1 @@
+*.aux
+*.bbl
+*.blg
+*.fdb*
+*.fls
+*.idx
+*.ilg
 *.ind
-*.ilg
+*.lo*
+*.out
+*.pdf
+*.pyg
+*.tdo
+*.toc
+*.xdv
+cache*

NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/NEMO/subfiles/chap_LBC.tex

@@ -5 +5 @@
 \chapter{Lateral Boundary Condition (LBC)}
 \label{chap:LBC}
-
-\thispagestyle{plain}
 
 \chaptertoc
@@ -161 +159 @@
 
 %% =================================================================================================
-\section[Model domain boundary condition (\forcode{jperio})]{Model domain boundary condition (\protect\jp{jperio})}
+\section{Model domain boundary condition}
 \label{sec:LBC_jperio}
 
@@ -170 +168 @@
 
 %% =================================================================================================
-\subsection[Closed, cyclic (\forcode{=0,1,2,7})]{Closed, cyclic (\protect\jp{jperio}\forcode{=0,1,2,7})}
+\subsection{Closed, cyclic (\forcode{l_Iperio,l_jperio})}
 \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}{cfg}.
+setting \forcode{l_Iperio,l_jperio} to true or false 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 $j=jpj-1$,
@@ -183 +181 @@
 \begin{description}
 
-\item [For closed boundary (\jp{jperio}\forcode{=0})], solid walls are imposed at all model boundaries:
+\item [For closed boundary (\forcode{l_Iperio = .false.,l_jperio = .false.})], 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 (\forcode{l_Iperio = .true.,l_jperio = .false.})], 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 (\forcode{l_Iperio = .false.,l_jperio = .true.})], 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 (\forcode{l_Iperio = .true.,l_jperio = .true.})] combines cases 1 and 2.
 
 \end{description}
@@ -209 +207 @@
 
 %% =================================================================================================
-\subsection[North-fold (\forcode{=3,6})]{North-fold (\protect\jp{jperio}\forcode{=3,6})}
+\subsection{North-fold (\forcode{l_NFold = .true.})}
 \label{subsec:LBC_north_fold}
 
@@ -222 +220 @@
   \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 ($jperio=4$),
+    North fold boundary with a $T$-point pivot and cyclic east-west boundary condition ($c\_NFtype='T'$),
     as used in ORCA 2\deg, 1/4\deg and 1/12\deg.
     Pink shaded area corresponds to the inner domain mask (see text).}
@@ -288 +286 @@
 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}.
+the main model dimensions are now the local dimensions of the subdomain (pencil) that are named \texttt{jpi}, \texttt{jpj}, \texttt{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 (nn\_hls=1, in \mdl{par\_oce},
+The number of rows to exchange (known as the halo) is usually set to one (\forcode{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 whole domain dimensions are named \texttt{jpiglo}, \texttt{jpjglo} and \texttt{jpk}.
 The relationship between the whole domain and a sub-domain is:
 \begin{gather*}
@@ -299 +297 @@
 \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.
+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 \texttt{jpi} is now always equal to nlci and \texttt{jpj} equal to nlcj.
 
 An element of $T_{l}$, a local array (subdomain) corresponds to an element of $T_{g}$,
@@ -309 +307 @@
 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 1-d arrays $mig(1:\texttt{jpi})$ and $mjg(1:\texttt{jpj})$, 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, $mi0(1:\texttt{jpiglo})$, $mi1(1:\texttt{jpiglo})$ and $mj0(1:\texttt{jpjglo})$, $mj1(1:\texttt{jpjglo})$ 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:
@@ -372 +370 @@
 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 \forcode{&nambdy_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.
+(\np[=.false.]{ln_coords_file}{ln\_coords\_file}, and a namelist block \forcode{&nambdy_index} must be included for each set) or read in from a file (\np[=.true.]{ln_coords_file}{ln\_coords\_file}, and a ``\textit{coordinates.bdy.nc}'' file must be provided).
+The coordinates.bdy file is analagous to the usual \NEMO\ ``\textit{coordinates.nc}'' 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 the namelist.
@@ -570 +568 @@
 
 The boundary geometry for each set may be defined in a namelist \forcode{&nambdy_index} or
-by reading in a ``\ifile{coordinates.bdy}'' file.
-The \texttt{nambdy\_index} namelist defines a series of straight-line segments for north, east, south and west boundaries.
-One \texttt{nambdy\_index} namelist block is needed for each boundary condition defined by indexes.
+by reading in a ``\textit{coordinates.bdy.nc}'' file.
+The \forcode{&nambdy_index} namelist defines a series of straight-line segments for north, east, south and west boundaries.
+One \forcode{&nambdy_index} namelist block is needed for each boundary condition defined by indexes.
 For the northern boundary, \texttt{nbdysegn} gives the number of segments,
-\jp{jpjnob} gives the $j$ index for each segment and \jp{jpindt} and
-\jp{jpinft} give the start and end $i$ indices for each segment with similar for the other boundaries.
+\texttt{jpjnob} gives the $j$ index for each segment and \texttt{jpindt} and
+\texttt{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[>1]{nn_rimwidth}{nn\_rimwidth}.
 
-The boundary geometry may also be defined from a ``\ifile{coordinates.bdy}'' file.
+The boundary geometry may also be defined from a ``\textit{coordinates.bdy.nc}'' file.
 \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.
@@ -633 +631 @@
   \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}
+  \caption[Header for a \textit{coordinates.bdy.nc} file]{
+    Example of the header for a \textit{coordinates.bdy.nc} file}
   \label{fig:LBC_nc_header}
 \end{figure}
@@ -684 +682 @@
 \texttt{<constituent>\_z1} and \texttt{<constituent>\_z2} for the real and imaginary parts of
 SSH, respectively, are expected to be available in file
-\ifile{<input>\_grid\_T}, variables \texttt{<constituent>\_u1} and
+\textit{<input>\_grid\_T.nc}, variables \texttt{<constituent>\_u1} and
 \texttt{<constituent>\_u2} for the real and imaginary parts of u, respectively, in file
-\ifile{<input>\_grid\_U}, and \texttt{<constituent>\_v1} and
+\textit{<input>\_grid\_U.nc}, and \texttt{<constituent>\_v1} and
 \texttt{<constituent>\_v2} for the real and imaginary parts of v, respectively, in file
-\ifile{<input>\_grid\_V}; when data along open boundary segments is used,
+\textit{<input>\_grid\_V.nc}; when data along open boundary segments is used,
 variables \texttt{z1} and \texttt{z2} (real and imaginary part of SSH) are
-expected to be available in file \ifile{<input><constituent>\_grid\_T},
+expected to be available in file \textit{<input><constituent>\_grid\_T.nc},
 variables \texttt{u1} and \texttt{u2} (real and imaginary part of u) in file
-\ifile{<input><constituent>\_grid\_U}, and variables \texttt{v1} and \texttt{v2}
+\textit{<input><constituent>\_grid\_U.nc}, and variables \texttt{v1} and \texttt{v2}
 (real and imaginary part of v) in file
-\ifile{<input><constituent>\_grid\_V}.\par
+\textit{<input><constituent>\_grid\_V.nc}.\par
 
 Note that the barotropic velocity components are assumed to be defined

@@ -9 +9 @@
 
 # SETTE
-^/utils/CI/sette_wave@13990         sette
+^/utils/CI/sette@14244        sette

@@ +1 @@
+*.aux
+*.bbl
+*.blg
+*.fdb*
+*.fls
+*.idx
+*.ilg
 *.ind
-*.ilg
+*.lo*
+*.out
+*.pdf
+*.pyg
+*.tdo
+*.toc
+*.xdv
+cache*