Index: branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_Model_Basics.tex
===================================================================
--- branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_Model_Basics.tex	(revision 5550)
+++ branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_Model_Basics.tex	(revision 6275)
@@ -247,75 +247,15 @@
 sufficient to solve a linearized version of (\ref{Eq_PE_ssh}), which still allows 
 to take into account freshwater fluxes applied at the ocean surface \citep{Roullet_Madec_JGR00}.
+Nevertheless, with the linearization, an exact conservation of heat and salt contents is lost.
 
 The filtering of EGWs in models with a free surface is usually a matter of discretisation 
-of the temporal derivatives, using the time splitting method \citep{Killworth_al_JPO91, Zhang_Endoh_JGR92} 
-or the implicit scheme \citep{Dukowicz1994}. In \NEMO, we use a slightly different approach 
-developed by \citet{Roullet_Madec_JGR00}: the damping of EGWs is ensured by introducing an 
-additional force in the momentum equation. \eqref{Eq_PE_dyn} becomes: 
-\begin{equation} \label{Eq_PE_flt}
-\frac{\partial {\rm {\bf U}}_h }{\partial t}= {\rm {\bf M}}
-- g \nabla \left( \tilde{\rho} \ \eta \right) 
-- g \ T_c \nabla \left( \widetilde{\rho} \ \partial_t \eta \right) 
-\end{equation}
-where $T_c$, is a parameter with dimensions of time which characterizes the force, 
-$\widetilde{\rho} = \rho / \rho_o$ is the dimensionless density, and $\rm {\bf M}$ 
-represents the collected contributions of the Coriolis, hydrostatic pressure gradient, 
-non-linear and viscous terms in \eqref{Eq_PE_dyn}.
-
-The new force can be interpreted as a diffusion of vertically integrated volume flux divergence. 
-The time evolution of $D$ is thus governed by a balance of two terms, $-g$ \textbf{A} $\eta$ 
-and $g \, T_c \,$ \textbf{A} $D$, associated with a propagative regime and a diffusive regime 
-in the temporal spectrum, respectively. In the diffusive regime, the EGWs no longer propagate, 
-$i.e.$ they are stationary and damped. The diffusion regime applies to the modes shorter than 
-$T_c$. For longer ones, the diffusion term vanishes. Hence, the temporally unresolved EGWs 
-can be damped by choosing $T_c > \rdt$. \citet{Roullet_Madec_JGR00} demonstrate that 
-(\ref{Eq_PE_flt}) can be integrated with a leap frog scheme except the additional term which 
-has to be computed implicitly. This is not surprising since the use of a large time step has a 
-necessarily numerical cost. Two gains arise in comparison with the previous formulations. 
-Firstly, the damping of EGWs can be quantified through the magnitude of the additional term. 
-Secondly, the numerical scheme does not need any tuning. Numerical stability is ensured as 
-soon as $T_c > \rdt$.
-
-When the variations of free surface elevation are small compared to the thickness of the first 
-model layer, the free surface equation (\ref{Eq_PE_ssh}) can be linearized. As emphasized 
-by \citet{Roullet_Madec_JGR00} the linearization of (\ref{Eq_PE_ssh}) has consequences on the 
-conservation of salt in the model. With the nonlinear free surface equation, the time evolution 
-of the total salt content is 
-\begin{equation} \label{Eq_PE_salt_content}
-    \frac{\partial }{\partial t}\int\limits_{D\eta } {S\;dv} 
-                        =\int\limits_S {S\;(-\frac{\partial \eta }{\partial t}-D+P-E)\;ds}
-\end{equation}
-where $S$ is the salinity, and the total salt is integrated over the whole ocean volume 
-$D_\eta$ bounded by the time-dependent free surface. The right hand side (which is an 
-integral over the free surface) vanishes when the nonlinear equation (\ref{Eq_PE_ssh}) 
-is satisfied, so that the salt is perfectly conserved. When the free surface equation is 
-linearized, \citet{Roullet_Madec_JGR00} show that the total salt content integrated in the fixed 
-volume $D$ (bounded by the surface $z=0$) is no longer conserved:
-\begin{equation} \label{Eq_PE_salt_content_linear}
-         \frac{\partial }{\partial t}\int\limits_D {S\;dv} 
-         		= - \int\limits_S {S\;\frac{\partial \eta }{\partial t}ds} 
-\end{equation}
-
-The right hand side of (\ref{Eq_PE_salt_content_linear}) is small in equilibrium solutions 
-\citep{Roullet_Madec_JGR00}. It can be significant when the freshwater forcing is not balanced and 
-the globally averaged free surface is drifting. An increase in sea surface height \textit{$\eta $} 
-results in a decrease of the salinity in the fixed volume $D$. Even in that case though, 
-the total salt integrated in the variable volume $D_{\eta}$ varies much less, since 
-(\ref{Eq_PE_salt_content_linear}) can be rewritten as 
-\begin{equation} \label{Eq_PE_salt_content_corrected}
-\frac{\partial }{\partial t}\int\limits_{D\eta } {S\;dv} 
-=\frac{\partial}{\partial t} \left[ \;{\int\limits_D {S\;dv} +\int\limits_S {S\eta \;ds} } \right]
-=\int\limits_S {\eta \;\frac{\partial S}{\partial t}ds}
-\end{equation}
-
-Although the total salt content is not exactly conserved with the linearized free surface, 
-its variations are driven by correlations of the time variation of surface salinity with the 
-sea surface height, which is a negligible term. This situation contrasts with the case of 
-the rigid lid approximation in which case freshwater forcing is represented by a virtual 
-salt flux, leading to a spurious source of salt at the ocean surface 
-\citep{Huang_JPO93, Roullet_Madec_JGR00}.
-
-\newpage
-$\ $\newline    % force a new ligne
+of the temporal derivatives, using a split-explicit method \citep{Killworth_al_JPO91, Zhang_Endoh_JGR92} 
+or the implicit scheme \citep{Dukowicz1994} or the addition of a filtering force in the momentum equation 
+\citep{Roullet_Madec_JGR00}. With the present release, \NEMO offers the choice between 
+an explicit free surface (see \S\ref{DYN_spg_exp}) or a split-explicit scheme strongly 
+inspired the one proposed by \citet{Shchepetkin_McWilliams_OM05} (see \S\ref{DYN_spg_ts}).
+
+%\newpage
+%$\ $\newline    % force a new line
 
 % ================================================================
@@ -773,10 +713,10 @@
 \end{equation}
 
-The equations solved by the ocean model \eqref{Eq_PE} in $s-$coordinate can be written as follows:
+The equations solved by the ocean model \eqref{Eq_PE} in $s-$coordinate can be written as follows (see Appendix~\ref{Apdx_A_momentum}):
 
  \vspace{0.5cm}
-* momentum equation:
+$\bullet$ Vector invariant form of the momentum equation :
 \begin{multline} \label{Eq_PE_sco_u}
-\frac{1}{e_3} \frac{\partial \left(  e_3\,u  \right) }{\partial t}=
+\frac{\partial  u   }{\partial t}=
 	+   \left( {\zeta +f} \right)\,v                                    
 	-   \frac{1}{2\,e_1} \frac{\partial}{\partial i} \left(  u^2+v^2   \right) 
@@ -787,5 +727,5 @@
 \end{multline}
 \begin{multline} \label{Eq_PE_sco_v}
-\frac{1}{e_3} \frac{\partial \left(  e_3\,v  \right) }{\partial t}=
+\frac{\partial v }{\partial t}=
 	-   \left( {\zeta +f} \right)\,u   
 	-   \frac{1}{2\,e_2 }\frac{\partial }{\partial j}\left(  u^2+v^2  \right)     	
@@ -795,9 +735,38 @@
 	+  D_v^{\vect{U}}  +   F_v^{\vect{U}} \quad
 \end{multline}
+
+ \vspace{0.5cm}
+$\bullet$ Vector invariant form of the momentum equation :
+\begin{multline} \label{Eq_PE_sco_u}
+\frac{1}{e_3} \frac{\partial \left(  e_3\,u  \right) }{\partial t}=
+   +   \left( { f + \frac{1}{e_1 \; e_2 }
+					\left( 	 v \frac{\partial e_2}{\partial i}
+						-u \frac{\partial e_1}{\partial j} 	\right)} 	\right) \, v    \\
+   - \frac{1}{e_1 \; e_2 \; e_3 } 	\left( 
+					\frac{\partial \left( {e_2 \, e_3 \, u\,u} \right)}{\partial i}
+		+			\frac{\partial \left( {e_1 \, e_3 \, v\,u} \right)}{\partial j}	\right)
+   - \frac{1}{e_3 }\frac{\partial \left( { \omega\,u} \right)}{\partial k}    \\
+	- \frac{1}{e_1} \frac{\partial}{\partial i} \left( \frac{p_s + p_h}{\rho _o}    \right)    
+	+  g\frac{\rho }{\rho _o}\sigma _1 
+	+   D_u^{\vect{U}}  +   F_u^{\vect{U}} \quad
+\end{multline}
+\begin{multline} \label{Eq_PE_sco_v}
+\frac{1}{e_3} \frac{\partial \left(  e_3\,v  \right) }{\partial t}=
+   -   \left( { f + \frac{1}{e_1 \; e_2}
+					\left( 	 v \frac{\partial e_2}{\partial i}
+						-u \frac{\partial e_1}{\partial j} 	\right)} 	\right) \, u   \\
+   - \frac{1}{e_1 \; e_2 \; e_3 } 	\left( 
+					\frac{\partial \left( {e_2 \; e_3  \,u\,v} \right)}{\partial i}
+		+			\frac{\partial \left( {e_1 \; e_3  \,v\,v} \right)}{\partial j}	\right)
+                 - \frac{1}{e_3 } \frac{\partial \left( { \omega\,v} \right)}{\partial k}    \\
+	-   \frac{1}{e_2 }\frac{\partial }{\partial j}\left( \frac{p_s+p_h }{\rho _o}  \right) 
+	 +  g\frac{\rho }{\rho _o }\sigma _2   
+	+  D_v^{\vect{U}}  +   F_v^{\vect{U}} \quad
+\end{multline}
+
 where the relative vorticity, \textit{$\zeta $}, the surface pressure gradient, and the hydrostatic 
 pressure have the same expressions as in $z$-coordinates although they do not represent 
 exactly the same quantities. $\omega$ is provided by the continuity equation 
 (see Appendix~\ref{Apdx_A}):
-
 \begin{equation} \label{Eq_PE_sco_continuity}
 \frac{\partial e_3}{\partial t} + e_3 \; \chi + \frac{\partial \omega }{\partial s} = 0   
@@ -809,5 +778,5 @@
 
  \vspace{0.5cm}
-* tracer equations:
+$\bullet$ tracer equations:
 \begin{multline} \label{Eq_PE_sco_t}
 \frac{1}{e_3} \frac{\partial \left(  e_3\,T  \right) }{\partial t}=
@@ -1024,5 +993,7 @@
 
 The $\tilde{z}$-coordinate has been developed by \citet{Leclair_Madec_OM10s}.
-It is not available in the current version of \NEMO.
+It is available in \NEMO since the version 3.4. Nevertheless, it is currently not robust enough 
+to be used in all possible configurations. Its use is therefore not recommended.
+
 
 \newpage 
@@ -1157,7 +1128,7 @@
 operator acting along $s-$surfaces (see \S\ref{LDF}).
 
-\subsubsection{Lateral second order tracer diffusive operator}
-
-The lateral second order tracer diffusive operator is defined by (see Appendix~\ref{Apdx_B}):
+\subsubsection{Lateral Laplacian tracer diffusive operator}
+
+The lateral Laplacian tracer diffusive operator is defined by (see Appendix~\ref{Apdx_B}):
 \begin{equation} \label{Eq_PE_iso_tensor}
 D^{lT}=\nabla {\rm {\bf .}}\left( {A^{lT}\;\Re \;\nabla T} \right) \qquad 
@@ -1180,8 +1151,10 @@
 ocean (see Appendix~\ref{Apdx_B}).
 
+For \textit{iso-level} diffusion, $r_1$ and $r_2 $ are zero. $\Re $ reduces to the identity 
+in the horizontal direction, no rotation is applied. 
+
 For \textit{geopotential} diffusion, $r_1$ and $r_2 $ are the slopes between the 
-geopotential and computational surfaces: in $z$-coordinates they are zero 
-($r_1 = r_2 = 0$) while in $s$-coordinate (including $\textit{z*}$ case) they are 
-equal to $\sigma _1$ and $\sigma _2$, respectively (see \eqref{Eq_PE_sco_slope} ).
+geopotential and computational surfaces: they are equal to $\sigma _1$ and $\sigma _2$, 
+respectively (see \eqref{Eq_PE_sco_slope} ).
 
 For \textit{isoneutral} diffusion $r_1$ and $r_2$ are the slopes between the isoneutral 
@@ -1231,19 +1204,17 @@
 to zero in the vicinity of the boundaries. The latter strategy is used in \NEMO (cf. Chap.~\ref{LDF}).
 
-\subsubsection{Lateral fourth order tracer diffusive operator}
-
-The lateral fourth order tracer diffusive operator is defined by:
+\subsubsection{Lateral bilaplacian tracer diffusive operator}
+
+The lateral bilaplacian tracer diffusive operator is defined by:
 \begin{equation} \label{Eq_PE_bilapT}
 D^{lT}=\Delta \left( {A^{lT}\;\Delta T} \right) 
 \qquad \text{where} \  D^{lT}=\Delta \left( {A^{lT}\;\Delta T} \right)
  \end{equation}
-
 It is the second order operator given by \eqref{Eq_PE_iso_tensor} applied twice with 
 the eddy diffusion coefficient correctly placed. 
 
-
-\subsubsection{Lateral second order momentum diffusive operator}
-
-The second order momentum diffusive operator along $z$- or $s$-surfaces is found by 
+\subsubsection{Lateral Laplacian momentum diffusive operator}
+
+The Laplacian momentum diffusive operator along $z$- or $s$-surfaces is found by 
 applying \eqref{Eq_PE_lap_vector} to the horizontal velocity vector (see Appendix~\ref{Apdx_B}):
 \begin{equation} \label{Eq_PE_lapU}
@@ -1279,5 +1250,5 @@
 of the Equator in a geographical coordinate system \citep{Lengaigne_al_JGR03}.
 
-\subsubsection{lateral fourth order momentum diffusive operator}
+\subsubsection{lateral bilaplacian momentum diffusive operator}
 
 As for tracers, the fourth order momentum diffusive operator along $z$ or $s$-surfaces 
