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

Timestamp:

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

Author:

nicolasmartin

Message:

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

File:

• NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex (modified) (35 diffs)

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

@@ -54 +54 @@
 (\np{ln_tra_trd}{ln\_tra\_trd} or \np[=.true.]{ln_tra_mxl}{ln\_tra\_mxl}), as described in \autoref{chap:DIA}.
 
+%% =================================================================================================
 \section[Tracer advection (\textit{traadv.F90})]{Tracer advection (\protect\mdl{traadv})}
 \label{sec:TRA_adv}
-%------------------------------------------namtra_adv-----------------------------------------------------
 
 \begin{listing}
@@ -63 +63 @@
   \label{lst:namtra_adv}
 \end{listing}
-%-------------------------------------------------------------------------------------------------------------
 
 When considered (\ie\ when \np{ln_traadv_OFF}{ln\_traadv\_OFF} is not set to \forcode{.true.}),
@@ -171 +170 @@
 their results.
 
+%% =================================================================================================
 \subsection[CEN: Centred scheme (\forcode{ln_traadv_cen})]{CEN: Centred scheme (\protect\np{ln_traadv_cen}{ln\_traadv\_cen})}
 \label{subsec:TRA_adv_cen}
@@ -235 +235 @@
 these near boundary grid points.
 
+%% =================================================================================================
 \subsection[FCT: Flux Corrected Transport scheme (\forcode{ln_traadv_fct})]{FCT: Flux Corrected Transport scheme (\protect\np{ln_traadv_fct}{ln\_traadv\_fct})}
 \label{subsec:TRA_adv_tvd}
@@ -274 +275 @@
 while a forward scheme is used for the diffusive part.
 
+%% =================================================================================================
 \subsection[MUSCL: Monotone Upstream Scheme for Conservative Laws (\forcode{ln_traadv_mus})]{MUSCL: Monotone Upstream Scheme for Conservative Laws (\protect\np{ln_traadv_mus}{ln\_traadv\_mus})}
 \label{subsec:TRA_adv_mus}
@@ -307 +309 @@
 (\np[=.true.]{ln_mus_ups}{ln\_mus\_ups}).
 
+%% =================================================================================================
 \subsection[UBS a.k.a. UP3: Upstream-Biased Scheme (\forcode{ln_traadv_ubs})]{UBS a.k.a. UP3: Upstream-Biased Scheme (\protect\np{ln_traadv_ubs}{ln\_traadv\_ubs})}
 \label{subsec:TRA_adv_ubs}
@@ -376 +379 @@
 Note the current version of \NEMO\ uses the computationally more efficient formulation \autoref{eq:TRA_adv_ubs}.
 
+%% =================================================================================================
 \subsection[QCK: QuiCKest scheme (\forcode{ln_traadv_qck})]{QCK: QuiCKest scheme (\protect\np{ln_traadv_qck}{ln\_traadv\_qck})}
 \label{subsec:TRA_adv_qck}
@@ -396 +400 @@
 %%%gmcomment   :  Cross term are missing in the current implementation....
 
+%% =================================================================================================
 \section[Tracer lateral diffusion (\textit{traldf.F90})]{Tracer lateral diffusion (\protect\mdl{traldf})}
 \label{sec:TRA_ldf}
-%-----------------------------------------nam_traldf------------------------------------------------------
 
 \begin{listing}
@@ -405 +409 @@
   \label{lst:namtra_ldf}
 \end{listing}
-%-------------------------------------------------------------------------------------------------------------
 
 Options are defined through the \nam{tra_ldf}{tra\_ldf} namelist variables.
@@ -425 +428 @@
 the pure vertical component is split into an explicit and an implicit part \citep{lemarie.debreu.ea_OM12}.
 
+%% =================================================================================================
 \subsection[Type of operator (\forcode{ln_traldf_}\{\forcode{OFF,lap,blp}\})]{Type of operator (\protect\np{ln_traldf_OFF}{ln\_traldf\_OFF}, \protect\np{ln_traldf_lap}{ln\_traldf\_lap}, or \protect\np{ln_traldf_blp}{ln\_traldf\_blp})}
 \label{subsec:TRA_ldf_op}
@@ -456 +460 @@
 whereas the laplacian damping time scales only like $\lambda^{-2}$.
 
+%% =================================================================================================
 \subsection[Action direction (\forcode{ln_traldf_}\{\forcode{lev,hor,iso,triad}\})]{Direction of action (\protect\np{ln_traldf_lev}{ln\_traldf\_lev}, \protect\np{ln_traldf_hor}{ln\_traldf\_hor}, \protect\np{ln_traldf_iso}{ln\_traldf\_iso}, or \protect\np{ln_traldf_triad}{ln\_traldf\_triad})}
 \label{subsec:TRA_ldf_dir}
@@ -479 +484 @@
 the next two sub-sections.
 
+%% =================================================================================================
 \subsection[Iso-level (bi-)laplacian operator (\forcode{ln_traldf_iso})]{Iso-level (bi-)laplacian operator ( \protect\np{ln_traldf_iso}{ln\_traldf\_iso})}
 \label{subsec:TRA_ldf_lev}
@@ -507 +513 @@
 They are calculated in the \mdl{zpshde} module, described in \autoref{sec:TRA_zpshde}.
 
+%% =================================================================================================
 \subsection{Standard and triad (bi-)laplacian operator}
 \label{subsec:TRA_ldf_iso_triad}
@@ -512 +519 @@
 %&&    Standard rotated (bi-)laplacian operator
 %&& ----------------------------------------------
+%% =================================================================================================
 \subsubsection[Standard rotated (bi-)laplacian operator (\textit{traldf\_iso.F90})]{Standard rotated (bi-)laplacian operator (\protect\mdl{traldf\_iso})}
 \label{subsec:TRA_ldf_iso}
@@ -555 +563 @@
 %&&     Triad rotated (bi-)laplacian operator
 %&&  -------------------------------------------
+%% =================================================================================================
 \subsubsection[Triad rotated (bi-)laplacian operator (\forcode{ln_traldf_triad})]{Triad rotated (bi-)laplacian operator (\protect\np{ln_traldf_triad}{ln\_traldf\_triad})}
 \label{subsec:TRA_ldf_triad}
@@ -573 +582 @@
 %&&    Option for the rotated operators
 %&& ----------------------------------------------
+%% =================================================================================================
 \subsubsection{Option for the rotated operators}
 \label{subsec:TRA_ldf_options}
@@ -584 +594 @@
 \end{itemize}
 
+%% =================================================================================================
 \section[Tracer vertical diffusion (\textit{trazdf.F90})]{Tracer vertical diffusion (\protect\mdl{trazdf})}
 \label{sec:TRA_zdf}
-%--------------------------------------------namzdf---------------------------------------------------------
-
-%--------------------------------------------------------------------------------------------------------------
+
 
 Options are defined through the \nam{zdf}{zdf} namelist variables.
@@ -618 +627 @@
 it overcomes the stability constraint.
 
+%% =================================================================================================
 \section{External forcing}
 \label{sec:TRA_sbc_qsr_bbc}
 
+%% =================================================================================================
 \subsection[Surface boundary condition (\textit{trasbc.F90})]{Surface boundary condition (\protect\mdl{trasbc})}
 \label{subsec:TRA_sbc}
@@ -686 +697 @@
 This is the reason why the modified filter is not applied in the linear free surface case (see \autoref{chap:TD}).
 
+%% =================================================================================================
 \subsection[Solar radiation penetration (\textit{traqsr.F90})]{Solar radiation penetration (\protect\mdl{traqsr})}
 \label{subsec:TRA_qsr}
-%--------------------------------------------namqsr--------------------------------------------------------
 
 \begin{listing}
@@ -695 +706 @@
   \label{lst:namtra_qsr}
 \end{listing}
-%--------------------------------------------------------------------------------------------------------------
 
 Options are defined through the \nam{tra_qsr}{tra\_qsr} namelist variables.
@@ -804 +814 @@
 \end{figure}
 
+%% =================================================================================================
 \subsection[Bottom boundary condition (\textit{trabbc.F90}) - \forcode{ln_trabbc})]{Bottom boundary condition (\protect\mdl{trabbc} - \protect\np{ln_trabbc}{ln\_trabbc})}
 \label{subsec:TRA_bbc}
-%--------------------------------------------nambbc--------------------------------------------------------
 
 \begin{listing}
@@ -813 +823 @@
   \label{lst:nambbc}
 \end{listing}
-%--------------------------------------------------------------------------------------------------------------
 \begin{figure}[!t]
   \centering
@@ -839 +848 @@
 the \ifile{geothermal\_heating} NetCDF file (\autoref{fig:TRA_geothermal}) \citep{emile-geay.madec_OS09}.
 
+%% =================================================================================================
 \section[Bottom boundary layer (\textit{trabbl.F90} - \forcode{ln_trabbl})]{Bottom boundary layer (\protect\mdl{trabbl} - \protect\np{ln_trabbl}{ln\_trabbl})}
 \label{sec:TRA_bbl}
-%--------------------------------------------nambbl---------------------------------------------------------
 
 \begin{listing}
@@ -848 +857 @@
   \label{lst:nambbl}
 \end{listing}
-%--------------------------------------------------------------------------------------------------------------
 
 Options are defined through the \nam{bbl}{bbl} namelist variables.
@@ -872 +880 @@
 \citet{campin.goosse_T99}.
 
+%% =================================================================================================
 \subsection[Diffusive bottom boundary layer (\forcode{nn_bbl_ldf=1})]{Diffusive bottom boundary layer (\protect\np[=1]{nn_bbl_ldf}{nn\_bbl\_ldf})}
 \label{subsec:TRA_bbl_diff}
@@ -908 +917 @@
 $\overline H^\sigma$, the along bottom mean temperature, salinity and depth, respectively.
 
+%% =================================================================================================
 \subsection[Advective bottom boundary layer (\forcode{nn_bbl_adv=1,2})]{Advective bottom boundary layer (\protect\np[=1,2]{nn_bbl_adv}{nn\_bbl\_adv})}
 \label{subsec:TRA_bbl_adv}
@@ -994 +1004 @@
 It has to be used to compute the effective velocity as well as the effective overturning circulation.
 
+%% =================================================================================================
 \section[Tracer damping (\textit{tradmp.F90})]{Tracer damping (\protect\mdl{tradmp})}
 \label{sec:TRA_dmp}
-%--------------------------------------------namtra_dmp-------------------------------------------------
 
 \begin{listing}
@@ -1003 +1013 @@
   \label{lst:namtra_dmp}
 \end{listing}
-%--------------------------------------------------------------------------------------------------------------
 
 In some applications it can be useful to add a Newtonian damping term into the temperature and salinity equations:
@@ -1050 +1059 @@
 \path{./tools/DMP_TOOLS}.
 
+%% =================================================================================================
 \section[Tracer time evolution (\textit{tranxt.F90})]{Tracer time evolution (\protect\mdl{tranxt})}
 \label{sec:TRA_nxt}
-%--------------------------------------------namdom-----------------------------------------------------
-%--------------------------------------------------------------------------------------------------------------
 
 Options are defined through the \nam{dom}{dom} namelist variables.
@@ -1082 +1090 @@
 $T^{t - \rdt} = T^t$ and $T^t = T_f$.
 
+%% =================================================================================================
 \section[Equation of state (\textit{eosbn2.F90})]{Equation of state (\protect\mdl{eosbn2})}
 \label{sec:TRA_eosbn2}
-%--------------------------------------------nameos-----------------------------------------------------
 
 \begin{listing}
@@ -1091 +1099 @@
   \label{lst:nameos}
 \end{listing}
-%--------------------------------------------------------------------------------------------------------------
-
+
+%% =================================================================================================
 \subsection[Equation of seawater (\forcode{ln_}\{\forcode{teos10,eos80,seos}\})]{Equation of seawater (\protect\np{ln_teos10}{ln\_teos10}, \protect\np{ln_teos80}{ln\_teos80}, or \protect\np{ln_seos}{ln\_seos})}
 \label{subsec:TRA_eos}
@@ -1212 +1220 @@
 \end{table}
 
+%% =================================================================================================
 \subsection[Brunt-V\"{a}is\"{a}l\"{a} frequency]{Brunt-V\"{a}is\"{a}l\"{a} frequency}
 \label{subsec:TRA_bn2}
@@ -1232 +1241 @@
 They are computed through \textit{eos\_rab}, a \fortran\ function that can be found in \mdl{eosbn2}.
 
+%% =================================================================================================
 \subsection{Freezing point of seawater}
 \label{subsec:TRA_fzp}
@@ -1251 +1261 @@
 a \fortran\ function that can be found in \mdl{eosbn2}.
 
+%% =================================================================================================
 %\subsection{Potential Energy anomalies}
 %\label{subsec:TRA_bn2}
@@ -1257 +1268 @@
 %
 
+%% =================================================================================================
 \section[Horizontal derivative in \textit{zps}-coordinate (\textit{zpshde.F90})]{Horizontal derivative in \textit{zps}-coordinate (\protect\mdl{zpshde})}
 \label{sec:TRA_zpshde}