Changeset 11597 for NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.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_ZDF.tex (modified) (35 diffs)

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

@@ -12 +12 @@
 %gm% Add here a small introduction to ZDF and naming of the different physics (similar to what have been written for TRA and DYN.
 
+%% =================================================================================================
 \section{Vertical mixing}
 \label{sec:ZDF}
@@ -38 +39 @@
 %and thus of the formulation used (see \autoref{chap:TD}).
 
-%--------------------------------------------namzdf--------------------------------------------------------
 
 \begin{listing}
@@ -45 +45 @@
   \label{lst:namzdf}
 \end{listing}
-%--------------------------------------------------------------------------------------------------------------
-
+
+%% =================================================================================================
 \subsection[Constant (\forcode{ln_zdfcst})]{Constant (\protect\np{ln_zdfcst}{ln\_zdfcst})}
 \label{subsec:ZDF_cst}
@@ -66 +66 @@
 $\sim10^{-9}~m^2.s^{-1}$ for salinity.
 
+%% =================================================================================================
 \subsection[Richardson number dependent (\forcode{ln_zdfric})]{Richardson number dependent (\protect\np{ln_zdfric}{ln\_zdfric})}
 \label{subsec:ZDF_ric}
 
-%--------------------------------------------namric---------------------------------------------------------
 
 \begin{listing}
@@ -76 +76 @@
   \label{lst:namzdf_ric}
 \end{listing}
-%--------------------------------------------------------------------------------------------------------------
 
 When \np[=.true.]{ln_zdfric}{ln\_zdfric}, a local Richardson number dependent formulation for the vertical momentum and
@@ -124 +123 @@
 the empirical values \np{rn_wtmix}{rn\_wtmix} and \np{rn_wvmix}{rn\_wvmix} \citep{lermusiaux_JMS01}.
 
+%% =================================================================================================
 \subsection[TKE turbulent closure scheme (\forcode{ln_zdftke})]{TKE turbulent closure scheme (\protect\np{ln_zdftke}{ln\_zdftke})}
 \label{subsec:ZDF_tke}
-%--------------------------------------------namzdf_tke--------------------------------------------------
 
 \begin{listing}
@@ -133 +132 @@
   \label{lst:namzdf_tke}
 \end{listing}
-%--------------------------------------------------------------------------------------------------------------
 
 The vertical eddy viscosity and diffusivity coefficients are computed from a TKE turbulent closure model based on
@@ -196 +194 @@
 \np{rn_avt0}{rn\_avt0} (\nam{zdf}{zdf} namelist, see \autoref{subsec:ZDF_cst}).
 
+%% =================================================================================================
 \subsubsection{Turbulent length scale}
 
@@ -266 +265 @@
 $\bar{e}$ reach its minimum value ($1.10^{-6}= C_k\, l_{min} \,\sqrt{\bar{e}_{min}}$ ).
 
+%% =================================================================================================
 \subsubsection{Surface wave breaking parameterization}
-%-----------------------------------------------------------------------%
 
 Following \citet{mellor.blumberg_JPO04}, the TKE turbulence closure model has been modified to
@@ -300 +299 @@
 surface $\bar{e}$ value.
 
+%% =================================================================================================
 \subsubsection{Langmuir cells}
-%--------------------------------------%
 
 Langmuir circulations (LC) can be described as ordered large-scale vertical motions in
@@ -354 +353 @@
 \]
 
+%% =================================================================================================
 \subsubsection{Mixing just below the mixed layer}
-%--------------------------------------------------------------%
 
 Vertical mixing parameterizations commonly used in ocean general circulation models tend to
@@ -402 +401 @@
 % (\eg\ Mellor, 1989; Large et al., 1994; Meier, 2001; Axell, 2002; St. Laurent and Garrett, 2002).
 
+%% =================================================================================================
 \subsection[GLS: Generic Length Scale (\forcode{ln_zdfgls})]{GLS: Generic Length Scale (\protect\np{ln_zdfgls}{ln\_zdfgls})}
 \label{subsec:ZDF_gls}
 
-%--------------------------------------------namzdf_gls---------------------------------------------------------
 
 \begin{listing}
@@ -412 +411 @@
   \label{lst:namzdf_gls}
 \end{listing}
-%--------------------------------------------------------------------------------------------------------------
 
 The Generic Length Scale (GLS) scheme is a turbulent closure scheme based on two prognostic equations:
@@ -463 +461 @@
 They are made available through the \np{nn_clo}{nn\_clo} namelist parameter.
 
-%--------------------------------------------------TABLE--------------------------------------------------
 \begin{table}[htbp]
   \centering
@@ -490 +487 @@
   \label{tab:ZDF_GLS}
 \end{table}
-%--------------------------------------------------------------------------------------------------------------
 
 In the Mellor-Yamada model, the negativity of $n$ allows to use a wall function to force the convergence of
@@ -522 +518 @@
  in \citet{reffray.guillaume.ea_GMD15} for the \NEMO\ model.
 
+%% =================================================================================================
 \subsection[OSM: OSMosis boundary layer scheme (\forcode{ln_zdfosm})]{OSM: OSMosis boundary layer scheme (\protect\np{ln_zdfosm}{ln\_zdfosm})}
 \label{subsec:ZDF_osm}
-%--------------------------------------------namzdf_osm---------------------------------------------------------
 
 \begin{listing}
@@ -531 +527 @@
   \label{lst:namzdf_osm}
 \end{listing}
-%--------------------------------------------------------------------------------------------------------------
 
 The OSMOSIS turbulent closure scheme is based on......   TBC
 
+%% =================================================================================================
 \subsection[ Discrete energy conservation for TKE and GLS schemes]{Discrete energy conservation for TKE and GLS schemes}
 \label{subsec:ZDF_tke_ene}
@@ -635 +631 @@
 %For the latter, it is in fact the ratio $\sqrt{\bar{e}}/l_\epsilon$ which is stored.
 
+%% =================================================================================================
 \section{Convection}
 \label{sec:ZDF_conv}
@@ -645 +642 @@
 or/and the use of a turbulent closure scheme.
 
+%% =================================================================================================
 \subsection[Non-penetrative convective adjustment (\forcode{ln_tranpc})]{Non-penetrative convective adjustment (\protect\np{ln_tranpc}{ln\_tranpc})}
 \label{subsec:ZDF_npc}
@@ -705 +703 @@
 having to recompute the expansion coefficients at each mixing iteration.
 
+%% =================================================================================================
 \subsection[Enhanced vertical diffusion (\forcode{ln_zdfevd})]{Enhanced vertical diffusion (\protect\np{ln_zdfevd}{ln\_zdfevd})}
 \label{subsec:ZDF_evd}
@@ -728 +727 @@
 a leapfrog environment \citep{leclair_phd10} (see \autoref{sec:TD_mLF}).
 
+%% =================================================================================================
 \subsection[Handling convection with turbulent closure schemes (\forcode{ln_zdf_}\{\forcode{tke,gls,osm}\})]{Handling convection with turbulent closure schemes (\forcode{ln_zdf{tke,gls,osm}})}
 \label{subsec:ZDF_tcs}
@@ -752 +752 @@
 % gm%  + one word on non local flux with KPP scheme trakpp.F90 module...
 
+%% =================================================================================================
 \section[Double diffusion mixing (\forcode{ln_zdfddm})]{Double diffusion mixing (\protect\np{ln_zdfddm}{ln\_zdfddm})}
 \label{subsec:ZDF_ddm}
 
-%-------------------------------------------namzdf_ddm-------------------------------------------------
 %
 %\nlst{namzdf_ddm}
-%--------------------------------------------------------------------------------------------------------------
 
 This parameterisation has been introduced in \mdl{zdfddm} module and is controlled by the namelist parameter
@@ -840 +839 @@
 This avoids duplication in the computation of $\alpha$ and $\beta$ (which is usually quite expensive).
 
+%% =================================================================================================
 \section[Bottom and top friction (\textit{zdfdrg.F90})]{Bottom and top friction (\protect\mdl{zdfdrg})}
 \label{sec:ZDF_drg}
 
-%--------------------------------------------namdrg--------------------------------------------------------
 %
 \begin{listing}
@@ -861 +860 @@
 \end{listing}
 
-%--------------------------------------------------------------------------------------------------------------
 
 Options to define the top and bottom friction are defined through the \nam{drg}{drg} namelist variables.
@@ -916 +914 @@
 Note than from \NEMO\ 4.0, drag coefficients are only computed at cell centers (\ie\ at T-points) and refer to as $c_b^T$ in the following. These are then linearly interpolated in space to get $c_b^\textbf{U}$ at velocity points.
 
+%% =================================================================================================
 \subsection[Linear top/bottom friction (\forcode{ln_lin})]{Linear top/bottom friction (\protect\np{ln_lin}{ln\_lin})}
 \label{subsec:ZDF_drg_linear}
@@ -952 +951 @@
 $mask\_value$ * \np{rn_boost}{rn\_boost} * \np{rn_Cd0}{rn\_Cd0}.
 
+%% =================================================================================================
 \subsection[Non-linear top/bottom friction (\forcode{ln_non_lin})]{Non-linear top/bottom friction (\protect\np{ln_non_lin}{ln\_non\_lin})}
 \label{subsec:ZDF_drg_nonlinear}
@@ -984 +984 @@
 $mask\_value$ * \np{rn_boost}{rn\_boost} * \np{rn_Cd0}{rn\_Cd0}.
 
+%% =================================================================================================
 \subsection[Log-layer top/bottom friction (\forcode{ln_loglayer})]{Log-layer top/bottom friction (\protect\np{ln_loglayer}{ln\_loglayer})}
 \label{subsec:ZDF_drg_loglayer}
@@ -1007 +1008 @@
 %In this case, the relevant namelist parameters are \np{rn_tfrz0}{rn\_tfrz0}, \np{rn_tfri2}{rn\_tfri2} and \np{rn_tfri2_max}{rn\_tfri2\_max}.
 
+%% =================================================================================================
 \subsection[Explicit top/bottom friction (\forcode{ln_drgimp=.false.})]{Explicit top/bottom friction (\protect\np[=.false.]{ln_drgimp}{ln\_drgimp})}
 \label{subsec:ZDF_drg_stability}
@@ -1065 +1067 @@
 The number of potential breaches of the explicit stability criterion are still reported for information purposes.
 
+%% =================================================================================================
 \subsection[Implicit top/bottom friction (\forcode{ln_drgimp=.true.})]{Implicit top/bottom friction (\protect\np[=.true.]{ln_drgimp}{ln\_drgimp})}
 \label{subsec:ZDF_drg_imp}
@@ -1092 +1095 @@
 Superscript $n+1$ means the velocity used in the friction formula is to be calculated, so it is implicit.
 
+%% =================================================================================================
 \subsection[Bottom friction with split-explicit free surface]{Bottom friction with split-explicit free surface}
 \label{subsec:ZDF_drg_ts}
@@ -1105 +1109 @@
 Note that other strategies are possible, like considering vertical diffusion step in advance, \ie\ prior barotropic integration.
 
+%% =================================================================================================
 \section[Internal wave-driven mixing (\forcode{ln_zdfiwm})]{Internal wave-driven mixing (\protect\np{ln_zdfiwm}{ln\_zdfiwm})}
 \label{subsec:ZDF_tmx_new}
 
-%--------------------------------------------namzdf_iwm------------------------------------------
 %
 \begin{listing}
@@ -1115 +1119 @@
   \label{lst:namzdf_iwm}
 \end{listing}
-%--------------------------------------------------------------------------------------------------------------
 
 The parameterization of mixing induced by breaking internal waves is a generalization of
@@ -1166 +1169 @@
 % Jc: input files names ?
 
+%% =================================================================================================
 \section[Surface wave-induced mixing (\forcode{ln_zdfswm})]{Surface wave-induced mixing (\protect\np{ln_zdfswm}{ln\_zdfswm})}
 \label{subsec:ZDF_swm}
@@ -1196 +1200 @@
 (for more information on wave parameters and settings see \autoref{sec:SBC_wave})
 
+%% =================================================================================================
 \section[Adaptive-implicit vertical advection (\forcode{ln_zad_Aimp})]{Adaptive-implicit vertical advection(\protect\np{ln_zad_Aimp}{ln\_zad\_Aimp})}
 \label{subsec:ZDF_aimp}
@@ -1319 +1324 @@
 \end{figure}
 
+%% =================================================================================================
 \subsection{Adaptive-implicit vertical advection in the OVERFLOW test-case}