Changeset 6497 for trunk

Timestamp:

2016-04-27T09:33:46+02:00 (8 years ago)

Author:

gm

Message:

#1720 - trunk: add Casimir tidal parameterization

Location:

trunk

Files:

• DOC/TexFiles/Chapters/Chap_DIA.tex (modified) (6 diffs)
• DOC/TexFiles/Chapters/Chap_DOM.tex (modified) (5 diffs)
• DOC/TexFiles/Chapters/Chap_SBC.tex (modified) (5 diffs)
• DOC/TexFiles/Chapters/Chap_STO.tex (modified) (1 diff)
• DOC/TexFiles/Chapters/Chap_TRA.tex (modified) (3 diffs)
• DOC/TexFiles/Chapters/Chap_ZDF.tex (modified) (9 diffs)
• DOC/TexFiles/Namelist/namzdf_tmx_new (added)
• NEMOGCM/CONFIG/SHARED/namelist_ref (modified) (33 diffs)
• NEMOGCM/NEMO/OPA_SRC/ZDF/zdfddm.F90 (modified) (1 diff)
• NEMOGCM/NEMO/OPA_SRC/ZDF/zdftke.F90 (modified) (3 diffs)
• NEMOGCM/NEMO/OPA_SRC/ZDF/zdftmx.F90 (modified) (1 diff)

trunk/DOC/TexFiles/Chapters/Chap_DIA.tex

@@ -1409 +1409 @@
 
 % -------------------------------------------------------------------------------------------------------------
-%       25 hour mean and hourly Surface, Mid and Bed 
-% -------------------------------------------------------------------------------------------------------------
-\section{25 hour mean output for tidal models }
-
-A module is available to compute a crudely detided M2 signal by obtaining a 25 hour mean.
-The 25 hour mean is available for daily runs by summing up the 25 hourly instantananeous hourly values from
-midnight at the start of the day to midight at the day end.
-This diagnostic is actived with the logical  $ln\_dia25h$
-
-%------------------------------------------nam_dia25h------------------------------------------------------
-\namdisplay{nam_dia25h}
-%----------------------------------------------------------------------------------------------------------
-
-\section{Top Middle and Bed hourly output }
-
-A module is available to output the surface (top), mid water and bed diagnostics of a set of standard variables. 
-This can be a useful diagnostic when hourly or sub-hourly output is required in high resolution tidal outputs.
-The tidal signal is retained but the overall data usage is cut to just three vertical levels. Also the bottom level 
-is calculated for each cell.
-This diagnostic is actived with the logical  $ln\_diatmb$
-
-%------------------------------------------nam_diatmb-----------------------------------------------------
-\namdisplay{nam_diatmb}
-%----------------------------------------------------------------------------------------------------------
-
-% -------------------------------------------------------------------------------------------------------------
 %       Sections transports
 % -------------------------------------------------------------------------------------------------------------
@@ -1440 +1414 @@
 \label{DIA_diag_dct}
 
+%------------------------------------------namdct----------------------------------------------------
+\namdisplay{namdct}
+%-------------------------------------------------------------------------------------------------------------
+
 A module is available to compute the transport of volume, heat and salt through sections. 
 This diagnostic is actived with \key{diadct}.
@@ -1459 +1437 @@
 and the time scales over which they are averaged, as well as the level of output for debugging:
 
-%------------------------------------------namdct----------------------------------------------------
-\namdisplay{namdct}
-%-------------------------------------------------------------------------------------------------------------
-
 \np{nn\_dct}: frequency of instantaneous transports computing
 
@@ -1469 +1443 @@
 \np{nn\_debug}: debugging of the section
 
-\subsubsection{ To create a binary file containing the pathway of each section }
-
-In \texttt{NEMOGCM/TOOLS/SECTIONS\_DIADCT/run}, the file \texttt{ {list\_sections.ascii\_global}}
+\subsubsection{ Creating a binary file containing the pathway of each section }
+
+In \texttt{NEMOGCM/TOOLS/SECTIONS\_DIADCT/run}, the file \textit{ {list\_sections.ascii\_global}}
 contains a list of all the sections that are to be computed (this list of sections is based on MERSEA project metrics).
 
@@ -1583 +1557 @@
 \texttt{=/0, =/ 1000.}   &  diagonal   & eastward  & westward  & postive: eastward  \\ \hline                
 \end{tabular}
-
-
-
-% -------------------------------------------------------------------------------------------------------------
-%       Other Diagnostics
-% -------------------------------------------------------------------------------------------------------------
-\section{Other Diagnostics (\key{diahth}, \key{diaar5})}
-\label{DIA_diag_others}
-
-
-Aside from the standard model variables, other diagnostics can be computed 
-on-line. The available ready-to-add diagnostics routines can be found in directory DIA. 
-Among the available diagnostics the following ones are obtained when defining 
-the \key{diahth} CPP key: 
-
-- the mixed layer depth (based on a density criterion \citep{de_Boyer_Montegut_al_JGR04}) (\mdl{diahth})
-
-- the turbocline depth (based on a turbulent mixing coefficient criterion) (\mdl{diahth})
-
-- the depth of the 20\deg C isotherm (\mdl{diahth})
-
-- the depth of the thermocline (maximum of the vertical temperature gradient) (\mdl{diahth})
-
-The poleward heat and salt transports, their advective and diffusive component, and 
-the meriodional stream function can be computed on-line in \mdl{diaptr} 
-\np{ln\_diaptr} to true (see the \textit{\ngn{namptr} } namelist below).  
-When \np{ln\_subbas}~=~true, transports and stream function are computed 
-for the Atlantic, Indian, Pacific and Indo-Pacific Oceans (defined north of 30\deg S) 
-as well as for the World Ocean. The sub-basin decomposition requires an input file 
-(\ifile{subbasins}) which contains three 2D mask arrays, the Indo-Pacific mask 
-been deduced from the sum of the Indian and Pacific mask (Fig~\ref{Fig_mask_subasins}). 
-
-%------------------------------------------namptr----------------------------------------------------
-\namdisplay{namptr} 
-%-------------------------------------------------------------------------------------------------------------
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-\begin{figure}[!t]     \begin{center}
-\includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_mask_subasins.pdf}
-\caption{   \label{Fig_mask_subasins}
-Decomposition of the World Ocean (here ORCA2) into sub-basin used in to compute
-the heat and salt transports as well as the meridional stream-function: Atlantic basin (red), 
-Pacific basin (green), Indian basin (bleue), Indo-Pacific basin (bleue+green). 
-Note that semi-enclosed seas (Red, Med and Baltic seas) as well as Hudson Bay 
-are removed from the sub-basins. Note also that the Arctic Ocean has been split 
-into Atlantic and Pacific basins along the North fold line.  }
-\end{center}   \end{figure}  
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-
-In addition, a series of diagnostics has been added in the \mdl{diaar5}. 
-They corresponds to outputs that are required for AR5 simulations 
-(see Section \ref{DIA_steric} below for one of them). 
-Activating those outputs requires to define the \key{diaar5} CPP key.
-\\
-\\
-
-\section{Courant numbers}
-Courant numbers provide a theoretical indication of the model's numerical stability. The advective Courant numbers can be calculated according to
-\begin{equation}
-\label{eq:CFL}
-C_u = |u|\frac{\rdt}{e_{1u}}, \quad C_v = |v|\frac{\rdt}{e_{2v}}, \quad C_w = |w|\frac{\rdt}{e_{3w}}
-\end{equation}
-in the zonal, meridional and vertical directions respectively. The vertical component is included although it is not strictly valid as the vertical velocity is calculated from the continuity equation rather than as a prognostic variable. Physically this represents the rate at which information is propogated across a grid cell. Values greater than 1 indicate that information is propagated across more than one grid cell in a single time step.
-
-The variables can be activated by setting the \np{nn\_diacfl} namelist parameter to 1 in the \ngn{namctl} namelist. The diagnostics will be written out to an ascii file named cfl\_diagnostics.ascii. In this file the maximum value of $C_u$, $C_v$, and $C_w$ are printed at each timestep along with the coordinates of where the maximum value occurs. At the end of the model run the maximum value of $C_u$, $C_v$, and $C_w$ for the whole model run is printed along with the coordinates of each. The maximum values from the run are also copied to the ocean.output file. 
 
 
@@ -1802 +1712 @@
 the \key{diaar5} defined to be called.
 
+
+
+% -------------------------------------------------------------------------------------------------------------
+%       Other Diagnostics
+% -------------------------------------------------------------------------------------------------------------
+\section{Other Diagnostics (\key{diahth}, \key{diaar5})}
+\label{DIA_diag_others}
+
+
+Aside from the standard model variables, other diagnostics can be computed on-line. 
+The available ready-to-add diagnostics modules can be found in directory DIA. 
+
+\subsection{Depth of various quantities (\mdl{diahth})}
+
+Among the available diagnostics the following ones are obtained when defining 
+the \key{diahth} CPP key: 
+
+- the mixed layer depth (based on a density criterion \citep{de_Boyer_Montegut_al_JGR04}) (\mdl{diahth})
+
+- the turbocline depth (based on a turbulent mixing coefficient criterion) (\mdl{diahth})
+
+- the depth of the 20\deg C isotherm (\mdl{diahth})
+
+- the depth of the thermocline (maximum of the vertical temperature gradient) (\mdl{diahth})
+
+% -----------------------------------------------------------
+%     Poleward heat and salt transports
+% -----------------------------------------------------------
+
+\subsection{Poleward heat and salt transports (\mdl{diaptr})}
+
+%------------------------------------------namptr-----------------------------------------
+\namdisplay{namptr} 
+%-----------------------------------------------------------------------------------------
+
+The poleward heat and salt transports, their advective and diffusive component, and 
+the meriodional stream function can be computed on-line in \mdl{diaptr} 
+\np{ln\_diaptr} to true (see the \textit{\ngn{namptr} } namelist below).  
+When \np{ln\_subbas}~=~true, transports and stream function are computed 
+for the Atlantic, Indian, Pacific and Indo-Pacific Oceans (defined north of 30\deg S) 
+as well as for the World Ocean. The sub-basin decomposition requires an input file 
+(\ifile{subbasins}) which contains three 2D mask arrays, the Indo-Pacific mask 
+been deduced from the sum of the Indian and Pacific mask (Fig~\ref{Fig_mask_subasins}). 
+
+%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+\begin{figure}[!t]     \begin{center}
+\includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_mask_subasins.pdf}
+\caption{   \label{Fig_mask_subasins}
+Decomposition of the World Ocean (here ORCA2) into sub-basin used in to compute
+the heat and salt transports as well as the meridional stream-function: Atlantic basin (red), 
+Pacific basin (green), Indian basin (bleue), Indo-Pacific basin (bleue+green). 
+Note that semi-enclosed seas (Red, Med and Baltic seas) as well as Hudson Bay 
+are removed from the sub-basins. Note also that the Arctic Ocean has been split 
+into Atlantic and Pacific basins along the North fold line.  }
+\end{center}   \end{figure}  
+%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+
+
+% -----------------------------------------------------------
+%       CMIP specific diagnostics 
+% -----------------------------------------------------------
+\subsection{CMIP specific diagnostics (\mdl{diaar5})}
+
+A series of diagnostics has been added in the \mdl{diaar5}. 
+They corresponds to outputs that are required for AR5 simulations (CMIP5)
+(see also Section \ref{DIA_steric} for one of them). 
+Activating those outputs requires to define the \key{diaar5} CPP key.
+
+
+% -----------------------------------------------------------
+%       25 hour mean and hourly Surface, Mid and Bed 
+% -----------------------------------------------------------
+\subsection{25 hour mean output for tidal models }
+
+%------------------------------------------nam_dia25h-------------------------------------
+\namdisplay{nam_dia25h}
+%-----------------------------------------------------------------------------------------
+
+A module is available to compute a crudely detided M2 signal by obtaining a 25 hour mean.
+The 25 hour mean is available for daily runs by summing up the 25 hourly instantananeous hourly values from
+midnight at the start of the day to midight at the day end.
+This diagnostic is actived with the logical  $ln\_dia25h$
+
+
+% -----------------------------------------------------------
+%     Top Middle and Bed hourly output
+% -----------------------------------------------------------
+\subsection{Top Middle and Bed hourly output }
+
+%------------------------------------------nam_diatmb-----------------------------------------------------
+\namdisplay{nam_diatmb}
+%----------------------------------------------------------------------------------------------------------
+
+A module is available to output the surface (top), mid water and bed diagnostics of a set of standard variables. 
+This can be a useful diagnostic when hourly or sub-hourly output is required in high resolution tidal outputs.
+The tidal signal is retained but the overall data usage is cut to just three vertical levels. Also the bottom level 
+is calculated for each cell.
+This diagnostic is actived with the logical  $ln\_diatmb$
+
+
+
+% -----------------------------------------------------------
+%     Courant numbers
+% -----------------------------------------------------------
+\subsection{Courant numbers}
+Courant numbers provide a theoretical indication of the model's numerical stability. The advective Courant numbers can be calculated according to
+\begin{equation}
+\label{eq:CFL}
+C_u = |u|\frac{\rdt}{e_{1u}}, \quad C_v = |v|\frac{\rdt}{e_{2v}}, \quad C_w = |w|\frac{\rdt}{e_{3w}}
+\end{equation}
+in the zonal, meridional and vertical directions respectively. The vertical component is included although it is not strictly valid as the vertical velocity is calculated from the continuity equation rather than as a prognostic variable. Physically this represents the rate at which information is propogated across a grid cell. Values greater than 1 indicate that information is propagated across more than one grid cell in a single time step.
+
+The variables can be activated by setting the \np{nn\_diacfl} namelist parameter to 1 in the \ngn{namctl} namelist. The diagnostics will be written out to an ascii file named cfl\_diagnostics.ascii. In this file the maximum value of $C_u$, $C_v$, and $C_w$ are printed at each timestep along with the coordinates of where the maximum value occurs. At the end of the model run the maximum value of $C_u$, $C_v$, and $C_w$ for the whole model run is printed along with the coordinates of each. The maximum values from the run are also copied to the ocean.output file. 
+
+
 % ================================================================
 

trunk/DOC/TexFiles/Chapters/Chap_DOM.tex

@@ -486 +486 @@
 The last choice in terms of vertical coordinate concerns the presence (or not) in the model domain 
 of ocean cavities beneath ice shelves. Setting \np{ln\_isfcav} to true allows to manage ocean cavities, 
-otherwise they are filled in.
+otherwise they are filled in. This option is currently only available in $z$- or $zps$-coordinate,
+and partial step are also applied at the ocean/ice shelf interface. 
 
 Contrary to the horizontal grid, the vertical grid is computed in the code and no 
@@ -772 +773 @@
 \end{equation}
 
-where $s_{min}$ is the depth at which the s-coordinate stretching starts and 
-allows a z-coordinate to placed on top of the stretched coordinate, 
-and z is the depth (negative down from the asea surface).
+where $s_{min}$ is the depth at which the $s$-coordinate stretching starts and 
+allows a $z$-coordinate to placed on top of the stretched coordinate, 
+and $z$ is the depth (negative down from the asea surface).
 
 \begin{equation}
@@ -886 +887 @@
 that do not communicate with another ocean point at the same level are eliminated.
 
-In case of ice shelf cavities, as for the representation of bathymetry, a 2D integer array, misfdep, is created. 
-misfdep defines the level of the first wet $t$-point (ie below the ice-shelf/ocean interface). All the cells between $k=1$ and $misfdep(i,j)-1$ are masked. 
-By default, $misfdep(:,:)=1$ and no cells are masked.
-Modifications of the model bathymetry and ice shelf draft into 
+As for the representation of bathymetry, a 2D integer array, misfdep, is created. 
+misfdep defines the level of the first wet $t$-point. All the cells between $k=1$ and $misfdep(i,j)-1$ are masked. 
+By default, misfdep(:,:)=1 and no cells are masked.
+
+In case of ice shelf cavities, modifications of the model bathymetry and ice shelf draft into 
 the cavities are performed in the \textit{zgr\_isf} routine. The compatibility between ice shelf draft and bathymetry is checked. 
 All the locations where the isf cavity is thinnest than \np{rn\_isfhmin} meters are grounded ($i.e.$ masked). 
@@ -903 +905 @@
 vmask(i,j,k) &=         \; tmask(i,j,k) \ * \ tmask(i,j+1,k)   \\
 fmask(i,j,k) &=         \; tmask(i,j,k) \ * \ tmask(i+1,j,k)   \\
-                   & \ \ \, * tmask(i,j,k) \ * \ tmask(i+1,j,k) \\
+             &    \ \ \, * tmask(i,j,k) \ * \ tmask(i+1,j,k) \\
 wmask(i,j,k) &=         \; tmask(i,j,k) \ * \ tmask(i,j,k-1) \text{ with } wmask(i,j,1) = tmask(i,j,1) 
 \end{align*}
 
-Note, wmask is now defined. It allows, in case of ice shelves, 
-to deal with the top boundary (ice shelf/ocean interface) exactly in the same way as for the bottom boundary. 
+Note that, without ice shelves cavities, masks at $t-$ and $w-$points are identical with 
+the numerical indexing used (\S~\ref{DOM_Num_Index}). Nevertheless, $wmask$ are required 
+with oceean cavities to deal with the top boundary (ice shelf/ocean interface) 
+exactly in the same way as for the bottom boundary. 
 
 The specification of closed lateral boundaries requires that at least the first and last 
@@ -916 +920 @@
 (and so too the mask arrays) (see \S~\ref{LBC_jperio}).
 
-%%%
-\gmcomment{   \colorbox{yellow}{Add one word on tricky trick !} mbathy in further modified in zdfbfr{\ldots}.  }
-%%%
 
 % ================================================================

trunk/DOC/TexFiles/Chapters/Chap_SBC.tex

@@ -128 +128 @@
 The ocean model provides, at each time step, to the surface module (\mdl{sbcmod}) 
 the surface currents, temperature and salinity.  
-These variables are averaged over \np{nf\_sbc} time-step (\ref{Tab_ssm}), 
+These variables are averaged over \np{nn\_fsbc} time-step (\ref{Tab_ssm}), 
 and it is these averaged fields which are used to computes the surface fluxes 
-at a frequency of \np{nf\_sbc} time-step.
+at a frequency of \np{nn\_fsbc} time-step.
 
 
@@ -144 +144 @@
 \caption{  \label{Tab_ssm}   
 Ocean variables provided by the ocean to the surface module (SBC). 
-The variable are averaged over nf{\_}sbc time step, $i.e.$ the frequency of 
-computation of surface fluxes.}
+The variable are averaged over nn{\_}fsbc time step, 
+$i.e.$ the frequency of computation of surface fluxes.}
 \end{center}   \end{table}
 %--------------------------------------------------------------------------------------------------------------
@@ -592 +592 @@
 or larger than the one of the input atmospheric fields.
 
+The \np{sn\_wndi}, \np{sn\_wndj}, \np{sn\_qsr}, \np{sn\_qlw}, \np{sn\_tair}, \np{sn\_humi},
+\np{sn\_prec}, \np{sn\_snow}, \np{sn\_tdif} parameters describe the fields 
+and the way they have to be used (spatial and temporal interpolations). 
+
+\np{cn\_dir} is the directory of location of bulk files
+\np{ln\_taudif} is the flag to specify if we use Hight Frequency (HF) tau information (.true.) or not (.false.)
+\np{rn\_zqt}: is the height of humidity and temperature measurements (m)
+\np{rn\_zu}: is the height of wind measurements (m)
+
+Three multiplicative factors are availables : 
+\np{rn\_pfac} and \np{rn\_efac} allows to adjust (if necessary) the global freshwater budget 
+by increasing/reducing the precipitations (total and snow) and or evaporation, respectively.
+The third one,\np{rn\_vfac}, control to which extend the ice/ocean velocities are taken into account 
+in the calculation of surface wind stress. Its range should be between zero and one, 
+and it is recommended to set it to 0.
+
 % -------------------------------------------------------------------------------------------------------------
 %        CLIO Bulk formulea
@@ -926 +942 @@
 \begin{description}
 \item[\np{nn\_isf}~=~1]
-The ice shelf cavity is represented (\np{ln\_isfcav}~=~true needed). The fwf and heat flux are computed. Two different bulk formula are available:
+The ice shelf cavity is represented (\np{ln\_isfcav}~=~true needed). The fwf and heat flux are computed. 
+Two different bulk formula are available:
    \begin{description}
    \item[\np{nn\_isfblk}~=~1]
@@ -988 +1005 @@
 This parameter is only used if \np{nn\_isf}~=~1 or \np{nn\_isf}~=~4
 
-If \np{rn\_hisf\_tbl} = 0.0, the fluxes are put in the top level whatever is its tickness. 
-
-If \np{rn\_hisf\_tbl} $>$ 0.0, the fluxes are spread over the first \np{rn\_hisf\_tbl} m (ie over one or several cells).\\
+If \np{rn\_hisf\_tbl} = 0., the fluxes are put in the top level whatever is its tickness. 
+
+If \np{rn\_hisf\_tbl} $>$ 0., the fluxes are spread over the first \np{rn\_hisf\_tbl} m (ie over one or several cells).\\
 
 The ice shelf melt is implemented as a volume flux with in the same way as for the runoff.

trunk/DOC/TexFiles/Chapters/Chap_STO.tex

@@ -5 +5 @@
 \label{STO}
 
+Authors: P.-A. Bouttier
+
 \minitoc
 
+\newpage
 
-\newpage
-$\ $\newline    % force a new line
+
+The stochastic parametrization module aims to explicitly simulate uncertainties in the model. 
+More particularly, \cite{Brankart_OM2013} has shown that, 
+because of the nonlinearity of the seawater equation of state, unresolved scales represent 
+a major source of uncertainties in the computation of the large scale horizontal density gradient 
+(from T/S large scale fields), and that the impact of these uncertainties can be simulated 
+by random processes representing unresolved T/S fluctuations.
+
+The stochastic formulation of the equation of state can be written as:
+\begin{equation}
+ \label{eq:eos_sto}
+  \rho = \frac{1}{2} \sum_{i=1}^m\{ \rho[T+\Delta T_i,S+\Delta S_i,p_o(z)] + \rho[T-\Delta T_i,S-\Delta S_i,p_o(z)] \}
+\end{equation}
+where $p_o(z)$ is the reference pressure depending on the depth and, 
+$\Delta T_i$ and $\Delta S_i$ are a set of T/S perturbations defined as the scalar product 
+of the respective local T/S gradients with random walks $\mathbf{\xi}$:
+\begin{equation}
+ \label{eq:sto_pert}
+ \Delta T_i = \mathbf{\xi}_i \cdot \nabla T \qquad \hbox{and} \qquad \Delta S_i = \mathbf{\xi}_i \cdot \nabla S
+\end{equation}
+$\mathbf{\xi}_i$ are produced by a first-order autoregressive processes (AR-1) with 
+a parametrized decorrelation time scale, and horizontal and vertical standard deviations $\sigma_s$. 
+$\mathbf{\xi}$ are uncorrelated over the horizontal and fully correlated along the vertical.
+
+
+\section{Stochastic processes}
+\label{STO_the_details}
+
+The starting point of our implementation of stochastic parameterizations
+in NEMO is to observe that many existing parameterizations are based
+on autoregressive processes, which are used as a basic source of randomness
+to transform a deterministic model into a probabilistic model.
+A generic approach is thus to add one single new module in NEMO,
+generating processes with appropriate statistics
+to simulate each kind of uncertainty in the model
+(see \cite{Brankart_al_GMD2015} for more details).
+
+In practice, at every model grid point, independent Gaussian autoregressive
+processes~$\xi^{(i)},\,i=1,\ldots,m$ are first generated
+using the same basic equation:
+
+\begin{equation}
+\label{eq:autoreg}
+\xi^{(i)}_{k+1} = a^{(i)} \xi^{(i)}_k + b^{(i)} w^{(i)} + c^{(i)}
+\end{equation}
+
+\noindent
+where $k$ is the index of the model timestep; and
+$a^{(i)}$, $b^{(i)}$, $c^{(i)}$ are parameters defining
+the mean ($\mu^{(i)}$) standard deviation ($\sigma^{(i)}$)
+and correlation timescale ($\tau^{(i)}$) of each process:
+
+\begin{itemize}
+\item for order~1 processes, $w^{(i)}$ is a Gaussian white noise,
+with zero mean and standard deviation equal to~1, and the parameters
+$a^{(i)}$, $b^{(i)}$, $c^{(i)}$ are given by:
+
+\begin{equation}
+\label{eq:ord1}
+\left\{
+\begin{array}{l}
+a^{(i)} = \varphi \\
+b^{(i)} = \sigma^{(i)} \sqrt{ 1 - \varphi^2 } 
+ \qquad\qquad\mbox{with}\qquad\qquad
+\varphi = \exp \left( - 1 / \tau^{(i)} \right) \\
+c^{(i)} = \mu^{(i)} \left( 1 - \varphi \right) \\
+\end{array}
+\right.
+\end{equation}
+
+\item for order~$n>1$ processes, $w^{(i)}$ is an order~$n-1$ autoregressive process,
+with zero mean, standard deviation equal to~$\sigma^{(i)}$; correlation timescale
+equal to~$\tau^{(i)}$; and the parameters $a^{(i)}$, $b^{(i)}$, $c^{(i)}$ are given by:
+
+\begin{equation}
+\label{eq:ord2}
+\left\{
+\begin{array}{l}
+a^{(i)} = \varphi \\
+b^{(i)} = \frac{n-1}{2(4n-3)} \sqrt{ 1 - \varphi^2 } 
+ \qquad\qquad\mbox{with}\qquad\qquad
+\varphi = \exp \left( - 1 / \tau^{(i)} \right) \\
+c^{(i)} = \mu^{(i)} \left( 1 - \varphi \right) \\
+\end{array}
+\right.
+\end{equation}
+
+\end{itemize}
+
+\noindent
+In this way, higher order processes can be easily generated recursively using 
+the same piece of code implementing Eq.~(\ref{eq:autoreg}), 
+and using succesively processes from order $0$ to~$n-1$ as~$w^{(i)}$.
+The parameters in Eq.~(\ref{eq:ord2}) are computed so that this recursive application
+of Eq.~(\ref{eq:autoreg}) leads to processes with the required standard deviation
+and correlation timescale, with the additional condition that
+the $n-1$ first derivatives of the autocorrelation function
+are equal to zero at~$t=0$, so that the resulting processes
+become smoother and smoother as $n$ is increased.
+
+Overall, this method provides quite a simple and generic way of generating 
+a wide class of stochastic processes. 
+However, this also means that new model parameters are needed to specify each of 
+these stochastic processes. As in any parameterization of lacking physics, 
+a very important issues then to tune these new parameters using either first principles, 
+model simulations, or real-world observations.
+
+\section{Implementation details}
+\label{STO_thech_details}
+
 %---------------------------------------namsbc--------------------------------------------------
 \namdisplay{namsto}
 %--------------------------------------------------------------------------------------------------------------
-$\ $\newline    % force a new ligne
 
+The computer code implementing stochastic parametrisations can be found in the STO directory.
+It involves three modules : 
+\begin{description}
+\item[\mdl{stopar}] : define the Stochastic parameters and their time evolution.
+\item[\mdl{storng}] : a random number generator based on (and includes) the 64-bit KISS 
+                      (Keep It Simple Stupid) random number generator distributed by George Marsaglia 
+                      (see \href{https://groups.google.com/forum/#!searchin/comp.lang.fortran/64-bit$20KISS$20RNGs}{here})
+\item[\mdl{stopts}] : stochastic parametrisation associated with the non-linearity of the equation of seawater, 
+ implementing Eq~\ref{eq:sto_pert} and specific piece of code in the equation of state implementing Eq~\ref{eq:eos_sto}.
+\end{description}
 
-See \cite{Brankart_OM2013} and \cite{Brankart_al_GMD2015} papers for a description of the parameterization.
+The \mdl{stopar} module has 3 public routines to be called by the model (in our case, NEMO):
+
+The first routine (\rou{sto\_par}) is a direct implementation of Eq.~(\ref{eq:autoreg}),
+applied at each model grid point (in 2D or 3D), 
+and called at each model time step ($k$) to update
+every autoregressive process ($i=1,\ldots,m$).
+This routine also includes a filtering operator, applied to $w^{(i)}$,
+to introduce a spatial correlation between the stochastic processes.
+
+The second routine (\rou{sto\_par\_init}) is an initialization routine mainly dedicated
+to the computation of parameters $a^{(i)}, b^{(i)}, c^{(i)}$
+for each autoregressive process, as a function of the statistical properties
+required by the model user (mean, standard deviation, time correlation,
+order of the process,\ldots). 
+
+Parameters for the processes can be specified through the following \ngn{namsto} namelist parameters:
+\begin{description}
+   \item[\np{nn\_sto\_eos}]   : number of independent random walks 
+   \item[\np{rn\_eos\_stdxy}] : random walk horz. standard deviation (in grid points)
+   \item[\np{rn\_eos\_stdz}]  : random walk vert. standard deviation (in grid points)
+   \item[\np{rn\_eos\_tcor}]  : random walk time correlation (in timesteps)
+   \item[\np{nn\_eos\_ord}]   : order of autoregressive processes
+   \item[\np{nn\_eos\_flt}]   : passes of Laplacian filter
+   \item[\np{rn\_eos\_lim}]   : limitation factor (default = 3.0)
+\end{description}
+This routine also includes the initialization (seeding) of the random number generator.
+
+The third routine (\rou{sto\_rst\_write}) writes a restart file (which suffix name is 
+given by \np{cn\_storst\_out} namelist parameter) containing the current value of 
+all autoregressive processes to allow restarting a simulation from where it has been interrupted.
+This file also contains the current state of the random number generator.
+When \np{ln\_rststo} is set to \textit{true}), the restart file (which suffix name is 
+given by \np{cn\_storst\_in} namelist parameter) is read by the initialization routine 
+(\rou{sto\_par\_init}). The simulation will continue exactly as if it was not interrupted
+only  when \np{ln\_rstseed} is set to \textit{true}, $i.e.$ when the state of 
+the random number generator is read in the restart file.

trunk/DOC/TexFiles/Chapters/Chap_TRA.tex

@@ -734 +734 @@
 (see \S\ref{SBC_rnf} for further detail of how it acts on temperature and salinity tendencies)
 
-$\bullet$ \textit{fwfisf}, the mass flux associated with ice shelf melt, (see \S\ref{SBC_isf} for further details 
-on how the ice shelf melt is computed and applied).
+$\bullet$ \textit{fwfisf}, the mass flux associated with ice shelf melt, 
+(see \S\ref{SBC_isf} for further details on how the ice shelf melt is computed and applied).
 
 The surface boundary condition on temperature and salinity is applied as follows:
@@ -840 +840 @@
 ($i.e.$ the inverses of the extinction length scales) are tabulated over 61 nonuniform 
 chlorophyll classes ranging from 0.01 to 10 g.Chl/L (see the routine \rou{trc\_oce\_rgb} 
-in \mdl{trc\_oce} module). Three types of chlorophyll can be chosen in the RGB formulation:
-(1) a constant 0.05 g.Chl/L value everywhere (\np{nn\_chdta}=0) ; (2) an observed 
-time varying chlorophyll (\np{nn\_chdta}=1) ; (3) simulated time varying chlorophyll
-by TOP biogeochemical model (\np{ln\_qsr\_bio}=true). In the latter case, the RGB 
-formulation is used to calculate both the phytoplankton light limitation in PISCES 
-or LOBSTER and the oceanic heating rate. 
-
+in \mdl{trc\_oce} module). Four types of chlorophyll can be chosen in the RGB formulation:
+\begin{description} 
+\item[\np{nn\_chdta}=0] 
+a constant 0.05 g.Chl/L value everywhere ; 
+\item[\np{nn\_chdta}=1]  
+an observed time varying chlorophyll deduced from satellite surface ocean color measurement 
+spread uniformly in the vertical direction ; 
+\item[\np{nn\_chdta}=2]  
+same as previous case except that a vertical profile of chlorophyl is used. 
+Following \cite{Morel_Berthon_LO89}, the profile is computed from the local surface chlorophyll value ;
+\item[\np{ln\_qsr\_bio}=true]  
+simulated time varying chlorophyll by TOP biogeochemical model. 
+In this case, the RGB formulation is used to calculate both the phytoplankton 
+light limitation in PISCES or LOBSTER and the oceanic heating rate. 
+\end{description} 
 The trend in \eqref{Eq_tra_qsr} associated with the penetration of the solar radiation 
 is added to the temperature trend, and the surface heat flux is modified in routine \mdl{traqsr}. 
@@ -1385 +1393 @@
                    I've changed "derivative" to "difference" and "mean" to "average"}
 
-With partial cells (\np{ln\_zps}=true) at bottom and top (\np{ln\_isfcav}=true), in general, tracers in horizontally 
-adjacent cells live at different depths. Horizontal gradients of tracers are needed 
-for horizontal diffusion (\mdl{traldf} module) and for the hydrostatic pressure 
-gradient (\mdl{dynhpg} module) to be active. The partial cell properties 
-at the top (\np{ln\_isfcav}=true) are computed in the same way as for the bottom. So, only the bottom interpolation is shown.
-\gmcomment{STEVEN from gm : question: not sure of  what -to be active- means}
+With partial cells (\np{ln\_zps}=true) at bottom and top (\np{ln\_isfcav}=true), in general, 
+tracers in horizontally adjacent cells live at different depths. 
+Horizontal gradients of tracers are needed for horizontal diffusion (\mdl{traldf} module) 
+and the hydrostatic pressure gradient calculations (\mdl{dynhpg} module). 
+The partial cell properties at the top (\np{ln\_isfcav}=true) are computed in the same way as for the bottom. 
+So, only the bottom interpolation is explained below.
 
 Before taking horizontal gradients between the tracers next to the bottom, a linear 

trunk/DOC/TexFiles/Chapters/Chap_ZDF.tex

@@ -262 +262 @@
 \end{equation}
 
-At the ocean surface, a non zero length scale is set through the  \np{rn\_lmin0} namelist 
+At the ocean surface, a non zero length scale is set through the  \np{rn\_mxl0} namelist 
 parameter. Usually the surface scale is given by $l_o = \kappa \,z_o$ 
 where $\kappa = 0.4$ is von Karman's constant and $z_o$ the roughness 
 parameter of the surface. Assuming $z_o=0.1$~m \citep{Craig_Banner_JPO94} 
-leads to a 0.04~m, the default value of \np{rn\_lsurf}. In the ocean interior 
+leads to a 0.04~m, the default value of \np{rn\_mxl0}. In the ocean interior 
 a minimum length scale is set to recover the molecular viscosity when $\bar{e}$ 
 reach its minimum value ($1.10^{-6}= C_k\, l_{min} \,\sqrt{\bar{e}_{min}}$ ).
@@ -295 +295 @@
 As the surface boundary condition on TKE is prescribed through $\bar{e}_o = e_{bb} |\tau| / \rho_o$, 
 with $e_{bb}$ the \np{rn\_ebb} namelist parameter, setting \np{rn\_ebb}~=~67.83 corresponds 
-to $\alpha_{CB} = 100$. further setting  \np{ln\_lsurf} to true applies \eqref{ZDF_Lsbc} 
-as surface boundary condition on length scale, with $\beta$ hard coded to the Stacet's value.
+to $\alpha_{CB} = 100$. Further setting  \np{ln\_mxl0} to true applies \eqref{ZDF_Lsbc} 
+as surface boundary condition on length scale, with $\beta$ hard coded to the Stacey's value.
 Note that a minimal threshold of \np{rn\_emin0}$=10^{-4}~m^2.s^{-2}$ (namelist parameters) 
 is applied on surface $\bar{e}$ value.
@@ -852 +852 @@
 The bottom friction represents the friction generated by the bathymetry. 
 The top friction represents the friction generated by the ice shelf/ocean interface. 
-As the friction processes at the top and bottom are represented similarly, only the bottom friction is described in detail below.\\
+As the friction processes at the top and bottom are treated in similar way, 
+only the bottom friction is described in detail below.
 
 
@@ -926 +927 @@
 $H = 4000$~m, the resulting friction coefficient is $r = 4\;10^{-4}$~m\;s$^{-1}$. 
 This is the default value used in \NEMO. It corresponds to a decay time scale 
-of 115~days. It can be changed by specifying \np{rn\_bfric1} (namelist parameter).
+of 115~days. It can be changed by specifying \np{rn\_bfri1} (namelist parameter).
 
 For the linear friction case the coefficients defined in the general 
@@ -936 +937 @@
 \end{split}
 \end{equation}
-When \np{nn\_botfr}=1, the value of $r$ used is \np{rn\_bfric1}. 
+When \np{nn\_botfr}=1, the value of $r$ used is \np{rn\_bfri1}. 
 Setting \np{nn\_botfr}=0 is equivalent to setting $r=0$ and leads to a free-slip 
 bottom boundary condition. These values are assigned in \mdl{zdfbfr}. 
@@ -943 +944 @@
 in the \ifile{bfr\_coef} input NetCDF file. The mask values should vary from 0 to 1. 
 Locations with a non-zero mask value will have the friction coefficient increased 
-by $mask\_value$*\np{rn\_bfrien}*\np{rn\_bfric1}.
+by $mask\_value$*\np{rn\_bfrien}*\np{rn\_bfri1}.
 
 % -------------------------------------------------------------------------------------------------------------
@@ -963 +964 @@
 $e_b = 2.5\;10^{-3}$m$^2$\;s$^{-2}$, while the FRAM experiment \citep{Killworth1992} 
 uses $C_D = 1.4\;10^{-3}$ and $e_b =2.5\;\;10^{-3}$m$^2$\;s$^{-2}$. 
-The CME choices have been set as default values (\np{rn\_bfric2} and \np{rn\_bfeb2} 
+The CME choices have been set as default values (\np{rn\_bfri2} and \np{rn\_bfeb2} 
 namelist parameters).
 
@@ -978 +979 @@
 \end{equation}
 
-The coefficients that control the strength of the non-linear bottom friction are 
-initialised as namelist parameters: $C_D$= \np{rn\_bfri2}, and $e_b$ =\np{rn\_bfeb2}. 
-Note for applications which treat tides explicitly a low or even zero value of 
-\np{rn\_bfeb2} is recommended. From v3.2 onwards a local enhancement of $C_D$ 
-is possible via an externally defined 2D mask array (\np{ln\_bfr2d}=true). 
-See previous section for details.
+The coefficients that control the strength of the non-linear bottom friction are
+initialised as namelist parameters: $C_D$= \np{rn\_bfri2}, and $e_b$ =\np{rn\_bfeb2}.
+Note for applications which treat tides explicitly a low or even zero value of
+\np{rn\_bfeb2} is recommended. From v3.2 onwards a local enhancement of $C_D$ is possible
+via an externally defined 2D mask array (\np{ln\_bfr2d}=true).  This works in the same way
+as for the linear bottom friction case with non-zero masked locations increased by
+$mask\_value$*\np{rn\_bfrien}*\np{rn\_bfri2}.
+
+% -------------------------------------------------------------------------------------------------------------
+%       Bottom Friction Log-layer
+% -------------------------------------------------------------------------------------------------------------
+\subsection{Log-layer Bottom Friction enhancement (\np{nn\_botfr} = 2, \np{ln\_loglayer} = .true.)}
+\label{ZDF_bfr_loglayer}
+
+In the non-linear bottom friction case, the drag coefficient, $C_D$, can be optionally
+enhanced using a "law of the wall" scaling. If  \np{ln\_loglayer} = .true., $C_D$ is no
+longer constant but is related to the thickness of the last wet layer in each column by:
+
+\begin{equation}
+C_D = \left ( {\kappa \over {\rm log}\left ( 0.5e_{3t}/rn\_bfrz0 \right ) } \right )^2
+\end{equation}
+
+\noindent where $\kappa$ is the von-Karman constant and \np{rn\_bfrz0} is a roughness
+length provided via the namelist.
+
+For stability, the drag coefficient is bounded such that it is kept greater or equal to
+the base \np{rn\_bfri2} value and it is not allowed to exceed the value of an additional
+namelist parameter: \np{rn\_bfri2\_max}, i.e.:
+
+\begin{equation}
+rn\_bfri2 \leq C_D \leq rn\_bfri2\_max
+\end{equation}
+
+\noindent Note also that a log-layer enhancement can also be applied to the top boundary
+friction if under ice-shelf cavities are in use (\np{ln\_isfcav}=.true.).  In this case, the
+relevant namelist parameters are \np{rn\_tfrz0}, \np{rn\_tfri2}
+and \np{rn\_tfri2\_max}.
 
 % -------------------------------------------------------------------------------------------------------------
@@ -1267 +1299 @@
 
 % ================================================================
+% Internal wave-driven mixing
+% ================================================================
+\section{Internal wave-driven mixing (\key{zdftmx\_new})}
+\label{ZDF_tmx_new}
+
+%--------------------------------------------namzdf_tmx_new------------------------------------------
+\namdisplay{namzdf_tmx_new}
+%--------------------------------------------------------------------------------------------------------------
+
+The parameterization of mixing induced by breaking internal waves is a generalization 
+of the approach originally proposed by \citet{St_Laurent_al_GRL02}. 
+A three-dimensional field of internal wave energy dissipation $\epsilon(x,y,z)$ is first constructed, 
+and the resulting diffusivity is obtained as 
+\begin{equation} \label{Eq_Kwave}
+A^{vT}_{wave} =  R_f \,\frac{ \epsilon }{ \rho \, N^2 }
+\end{equation}
+where $R_f$ is the mixing efficiency and $\epsilon$ is a specified three dimensional distribution 
+of the energy available for mixing. If the \np{ln\_mevar} namelist parameter is set to false, 
+the mixing efficiency is taken as constant and equal to 1/6 \citep{Osborn_JPO80}. 
+In the opposite (recommended) case, $R_f$ is instead a function of the turbulence intensity parameter 
+$Re_b = \frac{ \epsilon}{\nu \, N^2}$, with $\nu$ the molecular viscosity of seawater, 
+following the model of \cite{Bouffard_Boegman_DAO2013} 
+and the implementation of \cite{de_lavergne_JPO2016_efficiency}.
+Note that $A^{vT}_{wave}$ is bounded by $10^{-2}\,m^2/s$, a limit that is often reached when the mixing efficiency is constant.
+
+In addition to the mixing efficiency, the ratio of salt to heat diffusivities can chosen to vary 
+as a function of $Re_b$ by setting the \np{ln\_tsdiff} parameter to true, a recommended choice). 
+This parameterization of differential mixing, due to \cite{Jackson_Rehmann_JPO2014}, 
+is implemented as in \cite{de_lavergne_JPO2016_efficiency}.
+
+The three-dimensional distribution of the energy available for mixing, $\epsilon(i,j,k)$, is constructed 
+from three static maps of column-integrated internal wave energy dissipation, $E_{cri}(i,j)$, 
+$E_{pyc}(i,j)$, and $E_{bot}(i,j)$, combined to three corresponding vertical structures 
+(de Lavergne et al., in prep):
+\begin{align*}
+F_{cri}(i,j,k) &\propto e^{-h_{ab} / h_{cri} }\\
+F_{pyc}(i,j,k) &\propto N^{n\_p}\\
+F_{bot}(i,j,k) &\propto N^2 \, e^{- h_{wkb} / h_{bot} }
+\end{align*} 
+In the above formula, $h_{ab}$ denotes the height above bottom, 
+$h_{wkb}$ denotes the WKB-stretched height above bottom, defined by
+\begin{equation*}
+h_{wkb} = H \, \frac{ \int_{-H}^{z} N \, dz' } { \int_{-H}^{\eta} N \, dz'  } \; ,
+\end{equation*}
+The $n_p$ parameter (given by \np{nn\_zpyc} in \ngn{namzdf\_tmx\_new} namelist)  controls the stratification-dependence of the pycnocline-intensified dissipation. 
+It can take values of 1 (recommended) or 2.
+Finally, the vertical structures $F_{cri}$ and $F_{bot}$ require the specification of 
+the decay scales $h_{cri}(i,j)$ and $h_{bot}(i,j)$, which are defined by two additional input maps. 
+$h_{cri}$ is related to the large-scale topography of the ocean (etopo2) 
+and $h_{bot}$ is a function of the energy flux $E_{bot}$, the characteristic horizontal scale of 
+the abyssal hill topography \citep{Goff_JGR2010} and the latitude.
+
+% ================================================================
+
+
+

trunk/NEMOGCM/CONFIG/SHARED/namelist_ref

@@ -3 +3 @@
 !!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 !! NEMO/OPA  :  1 - run manager      (namrun)
-!! namelists    2 - Domain           (namcfg, namzgr, namzgr_sco, namdom, namtsd)
+!! namelists    2 - Domain           (namcfg, namzgr, namzgr_sco, namdom, namtsd, namcrs, namc1d, namc1d_uvd)
 !!              3 - Surface boundary (namsbc, namsbc_ana, namsbc_flx, namsbc_clio, namsbc_core, namsbc_sas
 !!                                    namsbc_cpl, namtra_qsr, namsbc_rnf,
@@ -59 +59 @@
 !!======================================================================
 !!   namcfg       parameters of the configuration
-!!   namzgr       vertical coordinate
+!!   namzgr       vertical coordinate                                   (default: NO selection)
 !!   namzgr_sco   s-coordinate or hybrid z-s-coordinate
 !!   namdom       space and time domain (bathymetry, mesh, timestep)
+!!   namwad       Wetting and drying                                    (default F)
+!!   namtsd       data: temperature & salinity
 !!   namcrs       coarsened grid (for outputs and/or TOP)               ("key_crs")
 !!   namc1d       1D configuration options                              ("key_c1d")
+!!   namc1d_dyndmp 1D newtonian damping applied on currents             ("key_c1d")
 !!   namc1d_uvd   1D data (currents)                                    ("key_c1d")
-!!   namc1d_dyndmp 1D newtonian damping applied on currents             ("key_c1d")
-!!   namtsd       data: temperature & salinity
 !!======================================================================
 !
@@ -101 +102 @@
 /
 !-----------------------------------------------------------------------
-&namzgr_sco    !   s-coordinate or hybrid z-s-coordinate
+&namzgr_sco    !   s-coordinate or hybrid z-s-coordinate                (default F)
 !-----------------------------------------------------------------------
    ln_s_sh94   = .false.    !  Song & Haidvogel 1994 hybrid S-sigma   (T)|
@@ -165 +166 @@
 /
 !-----------------------------------------------------------------------
+&namwad        !   Wetting and drying                                   (default F)
+!-----------------------------------------------------------------------
+   ln_wd       = .false.   !  T/F activation of wetting and drying
+   rn_wdmin1   =  0.1      !  Minimum wet depth on dried cells
+   rn_wdmin2   =  0.01     !  Tolerance of min wet depth on dried cells
+   rn_wdld     =  20.0     !  Land elevation below which wetting/drying is allowed
+   nn_wdit     =  10       !  Max iterations for W/D limiter
+/
+!-----------------------------------------------------------------------
+&namtsd        !   data : Temperature  & Salinity
+!-----------------------------------------------------------------------
+!              !  file name                 ! frequency (hours) ! variable ! time interp.!  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!              !                            !  (if <0  months)  !   name   !  (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
+   sn_tem = 'data_1m_potential_temperature_nomask',     -1      ,'votemper',   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    ''
+   sn_sal = 'data_1m_salinity_nomask'             ,     -1      ,'vosaline',   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    ''
+   !
+   cn_dir      = './'      !  root directory for the location of the runoff files
+   ln_tsd_init = .true.    !  Initialisation of ocean T & S with T & S input data (T) or not (F)
+   ln_tsd_tradmp = .true.  !  damping of ocean T & S toward T & S input data (T) or not (F)
+/
+!-----------------------------------------------------------------------
 &namcrs        !   coarsened grid (for outputs and/or TOP)              ("key_crs")
 !-----------------------------------------------------------------------
@@ -202 +224 @@
    ln_uvd_init   = .false. !  Initialisation of ocean U & V with U & V input data (T) or not (F)
    ln_uvd_dyndmp = .false. !  damping of ocean U & V toward U & V input data (T) or not (F)
-/
-!-----------------------------------------------------------------------
-&namtsd    !   data : Temperature  & Salinity
-!-----------------------------------------------------------------------
-!          !  file name                            ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
-!          !                                       !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
-   sn_tem  = 'data_1m_potential_temperature_nomask',         -1        ,'votemper' ,    .true.    , .true. , 'yearly'   , ''       ,   ''    ,    ''
-   sn_sal  = 'data_1m_salinity_nomask'             ,         -1        ,'vosaline' ,    .true.    , .true. , 'yearly'   , ''       ,   ''    ,    ''
-   !
-   cn_dir        = './'     !  root directory for the location of the runoff files
-   ln_tsd_init   = .true.   !  Initialisation of ocean T & S with T &S input data (T) or not (F)
-   ln_tsd_tradmp = .true.   !  damping of ocean T & S toward T &S input data (T) or not (F)
 /
 
@@ -278 +288 @@
    ln_apr_dyn  = .false.   !  Patm gradient added in ocean & ice Eqs.   (T => fill namsbc_apr )
    ln_isf      = .false.   !  ice shelf                                 (T   => fill namsbc_isf)
-   ln_wave = .false.       !  coupling with surface wave                (T => fill namsbc_wave)
-   nn_lsm  = 0             !  =0 land/sea mask for input fields is not applied (keep empty land/sea mask filename field) ,
+   ln_wave     = .false.   !  coupling with surface wave                (T => fill namsbc_wave)
+   nn_lsm      = 0         !  =0 land/sea mask for input fields is not applied (keep empty land/sea mask filename field) ,
                            !  =1:n number of iterations of land/sea mask application for input fields (fill land/sea mask filename field)
 /
@@ -382 +392 @@
    sn_rcv_co2    =   'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
 !
-   nn_cplmodel   =     1     !  Maximum number of models to/from which NEMO is potentialy sending/receiving data
-   ln_usecplmask = .false.   !  use a coupling mask file to merge data received from several models
-                             !   -> file cplmask.nc with the float variable called cplmask (jpi,jpj,nn_cplmodel)
+   nn_cplmodel   =     1   !  Maximum number of models to/from which NEMO is potentialy sending/receiving data
+   ln_usecplmask = .false. !  use a coupling mask file to merge data received from several models
+   !                       !   -> file cplmask.nc with the float variable called cplmask (jpi,jpj,nn_cplmodel)
 /
 !-----------------------------------------------------------------------
 &namsbc_sas    !   analytical surface boundary condition
 !-----------------------------------------------------------------------
-!              !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
-!              !             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
-   sn_usp      = 'sas_grid_U' ,    120           , 'vozocrtx' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
-   sn_vsp      = 'sas_grid_V' ,    120           , 'vomecrty' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
-   sn_tem      = 'sas_grid_T' ,    120           , 'sosstsst' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
-   sn_sal      = 'sas_grid_T' ,    120           , 'sosaline' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
-   sn_ssh      = 'sas_grid_T' ,    120           , 'sossheig' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
-   sn_e3t      = 'sas_grid_T' ,    120           , 'e3t_m'    ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
-   sn_frq      = 'sas_grid_T' ,    120           , 'frq_m'    ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
+!              !  file name  ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!              !             !  (if <0  months)  !   name    !  (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
+   sn_usp      = 'sas_grid_U',     120           , 'vozocrtx',   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    ''
+   sn_vsp      = 'sas_grid_V',     120           , 'vomecrty',   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    ''
+   sn_tem      = 'sas_grid_T',     120           , 'sosstsst',   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    ''
+   sn_sal      = 'sas_grid_T',     120           , 'sosaline',   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    ''
+   sn_ssh      = 'sas_grid_T',     120           , 'sossheig',   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    ''
+   sn_e3t      = 'sas_grid_T',     120           , 'e3t_m'   ,   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    ''
+   sn_frq      = 'sas_grid_T',     120           , 'frq_m'   ,   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    ''
 
    ln_3d_uve   = .true.    !  specify whether we are supplying a 3D u,v and e3 field
-   ln_read_frq = .false.    !  specify whether we must read frq or not
+   ln_read_frq = .false.   !  specify whether we must read frq or not
    cn_dir      = './'      !  root directory for the location of the bulk files are
 /
@@ -431 +441 @@
    sn_dep_rnf  = 'runoffs'            ,         0         , 'rodepth' ,   .false.    , .true. , 'yearly'  , ''       , ''       , ''
 
-   cn_dir       = './'      !  root directory for the location of the runoff files
-   ln_rnf_mouth = .true.    !  specific treatment at rivers mouths
-   rn_hrnf      =  15.e0    !  depth over which enhanced vertical mixing is used
-   rn_avt_rnf   =   1.e-3   !  value of the additional vertical mixing coef. [m2/s]
-   rn_rfact     =   1.e0    !  multiplicative factor for runoff
-   ln_rnf_depth = .false.   !  read in depth information for runoff
-   ln_rnf_tem   = .false.   !  read in temperature information for runoff
-   ln_rnf_sal   = .false.   !  read in salinity information for runoff
-   ln_rnf_depth_ini = .false.  ! compute depth at initialisation from runoff file
-   rn_rnf_max   = 5.735e-4  !  max value of the runoff climatologie over global domain ( ln_rnf_depth_ini = .true )
-   rn_dep_max   = 150.      !  depth over which runoffs is spread ( ln_rnf_depth_ini = .true )
-   nn_rnf_depth_file = 0    !  create (=1) a runoff depth file or not (=0)
+   cn_dir      = './'      !  root directory for the location of the runoff files
+   ln_rnf_mouth= .true.    !  specific treatment at rivers mouths
+      rn_hrnf     =  15.e0    !  depth over which enhanced vertical mixing is used    (ln_rnf_mouth=T)
+      rn_avt_rnf  =   1.e-3   !  value of the additional vertical mixing coef. [m2/s] (ln_rnf_mouth=T)
+   rn_rfact    =   1.e0    !  multiplicative factor for runoff
+   ln_rnf_depth= .false.   !  read in depth information for runoff
+   ln_rnf_tem  = .false.   !  read in temperature information for runoff
+   ln_rnf_sal  = .false.   !  read in salinity information for runoff
+   ln_rnf_depth_ini = .false. ! compute depth at initialisation from runoff file
+      rn_rnf_max  = 5.735e-4  !  max value of the runoff climatologie over global domain ( ln_rnf_depth_ini = .true )
+      rn_dep_max  = 150.      !  depth over which runoffs is spread ( ln_rnf_depth_ini = .true )
+      nn_rnf_depth_file = 0   !  create (=1) a runoff depth file or not (=0)
 /
 !-----------------------------------------------------------------------
 &namsbc_isf    !  Top boundary layer (ISF)                              (nn_isf >0)
 !-----------------------------------------------------------------------
-!              ! file name ! frequency (hours) ! variable ! time interp. !  clim   ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
-!              !           !  (if <0  months)  !   name   !  (logical)   !  (T/F)  ! 'monthly' ! filename ! pairing  ! filename      !
+!              ! file name ! frequency (hours) ! variable ! time interp.!  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!              !           !  (if <0  months)  !   name   !  (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
 ! nn_isf == 4
-   sn_fwfisf   = 'rnfisf'  ,         -12       ,'sowflisf',   .false.    , .true.  , 'yearly'  ,  ''      ,   ''     , ''
+   sn_fwfisf   = 'rnfisf'  ,         -12       ,'sowflisf',   .false.   , .true. , 'yearly'  ,    ''    ,   ''     ,    ''
 ! nn_isf == 3
-   sn_rnfisf   = 'rnfisf'  ,         -12       ,'sofwfisf',   .false.    , .true.  , 'yearly'  ,  ''      ,   ''     , ''
+   sn_rnfisf   = 'rnfisf'  ,         -12       ,'sofwfisf',   .false.   , .true. , 'yearly'  ,    ''    ,   ''     ,    ''
 ! nn_isf == 2 and 3
-   sn_depmax_isf='rnfisf'  ,         -12       ,'sozisfmax',  .false.    , .true.  , 'yearly'  ,  ''      ,   ''     , ''
-   sn_depmin_isf='rnfisf'  ,         -12       ,'sozisfmin',  .false.    , .true.  , 'yearly'  ,  ''      ,   ''     , ''
+   sn_depmax_isf='rnfisf'  ,         -12       ,'sozisfmax',  .false.   , .true. , 'yearly'  ,    ''    ,   ''     ,    ''
+   sn_depmin_isf='rnfisf'  ,         -12       ,'sozisfmin',  .false.   , .true. , 'yearly'  ,    ''    ,   ''     ,    ''
 ! nn_isf == 2
-   sn_Leff_isf = 'rnfisf'  ,         -12       ,'Leff'    ,   .false.    , .true.  , 'yearly'  ,  ''      ,   ''     , ''
+   sn_Leff_isf = 'rnfisf'  ,         -12       ,'Leff'    ,   .false.   , .true. , 'yearly'  ,    ''    ,   ''     ,    ''
 !
 ! for all case
@@ -465 +475 @@
                            !  option 1 and 4 need ln_isfcav = .true. (domzgr)
 ! only for nn_isf = 1 or 2
-   rn_gammat0  = 1.e-4    ! gammat coefficient used in blk formula
-   rn_gammas0  = 1.e-4    ! gammas coefficient used in blk formula
+   rn_gammat0  = 1.e-4     ! gammat coefficient used in blk formula
+   rn_gammas0  = 1.e-4     ! gammas coefficient used in blk formula
 ! only for nn_isf = 1 or 4
    rn_hisf_tbl =  30.      ! thickness of the top boundary layer    (Losh et al. 2008)
-                          ! 0 => thickness of the tbl = thickness of the first wet cell
+   !                       ! 0 => thickness of the tbl = thickness of the first wet cell
 ! only for nn_isf = 1
-   nn_isfblk   = 1        ! 1 ISOMIP  like: 2 equations formulation (Hunter et al., 2006)
-                          ! 2 ISOMIP+ like: 3 equations formulation (Asay-Davis et al., 2015)
-   nn_gammablk = 1        ! 0 = cst Gammat (= gammat/s)
-                          ! 1 = velocity dependend Gamma (u* * gammat/s)  (Jenkins et al. 2010)
-                          ! 2 = velocity and stability dependent Gamma    (Holland et al. 1999)
+   nn_isfblk   = 1         ! 1 ISOMIP  like: 2 equations formulation (Hunter et al., 2006)
+   !                       ! 2 ISOMIP+ like: 3 equations formulation (Asay-Davis et al., 2015)
+   nn_gammablk = 1         ! 0 = cst Gammat (= gammat/s)
+   !                       ! 1 = velocity dependend Gamma (u* * gammat/s)  (Jenkins et al. 2010)
+   !                       ! 2 = velocity and stability dependent Gamma    (Holland et al. 1999)
 /
 !-----------------------------------------------------------------------
 &namsbc_iscpl  !   land ice / ocean coupling option                     
 !-----------------------------------------------------------------------
-   nn_drown  = 10       ! number of iteration of the extrapolation loop (fill the new wet cells)
-   ln_hsb    = .false.  ! activate conservation module (conservation exact after a time of rn_fiscpl)
-   nn_fiscpl = 43800    ! (number of time step) conservation period (maybe should be fix to the coupling frequencey of restart frequency)
+   nn_drown    = 10        ! number of iteration of the extrapolation loop (fill the new wet cells)
+   ln_hsb      = .false.   ! activate conservation module (conservation exact after a time of rn_fiscpl)
+   nn_fiscpl   = 43800     ! (number of time step) conservation period (maybe should be fix to the coupling frequencey of restart frequency)
 /
 !-----------------------------------------------------------------------
 &namsbc_apr    !   Atmospheric pressure used as ocean forcing or in bulk
 !-----------------------------------------------------------------------
-!              !  file name ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
-!              !            !  (if <0  months)  !   name    !  (logical)   !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
-   sn_apr      = 'patm'     ,         -1        ,'somslpre',    .true.     , .true. , 'yearly'  ,  ''      ,   ''     , ''
-
-   cn_dir      = './'       !  root directory for the location of the bulk files
-   rn_pref     = 101000.    !  reference atmospheric pressure   [N/m2]/
-   ln_ref_apr  = .false.    !  ref. pressure: global mean Patm (T) or a constant (F)
-   ln_apr_obc  = .false.    !  inverse barometer added to OBC ssh data
+!              ! file name ! frequency (hours) ! variable ! time interp.!  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!              !           !  (if <0  months)  !   name   !  (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
+   sn_apr      = 'patm'    ,         -1        ,'somslpre',   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,      ''
+
+   cn_dir      = './'      !  root directory for the location of the bulk files
+   rn_pref     = 101000.   !  reference atmospheric pressure   [N/m2]/
+   ln_ref_apr  = .false.   !  ref. pressure: global mean Patm (T) or a constant (F)
+   ln_apr_obc  = .false.   !  inverse barometer added to OBC ssh data
 /
 !-----------------------------------------------------------------------
 &namsbc_ssr    !   surface boundary condition : sea surface restoring   (ln_ssr=T)
 !-----------------------------------------------------------------------
-!              !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
-!              !             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
-   sn_sst      = 'sst_data'  ,        24         ,  'sst'    ,    .false.   , .false., 'yearly'  , ''       , ''       , ''
-   sn_sss      = 'sss_data'  ,        -1         ,  'sss'    ,    .true.    , .true. , 'yearly'  , ''       , ''       , ''
+!              ! file name ! frequency (hours) ! variable ! time interp.!  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!              !           !  (if <0  months)  !   name   !   (logical) !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
+   sn_sst      = 'sst_data',        24         ,  'sst'   ,    .false.  , .false., 'yearly'  ,    ''    ,    ''    ,     ''
+   sn_sss      = 'sss_data',        -1         ,  'sss'   ,    .true.   , .true. , 'yearly'  ,    ''    ,    ''    ,     ''
 
    cn_dir      = './'      !  root directory for the location of the runoff files
@@ -510 +520 @@
    rn_dqdt     =   -40.    !  magnitude of the retroaction on temperature   [W/m2/K]
    rn_deds     =  -166.67  !  magnitude of the damping on salinity   [mm/day]
-   ln_sssr_bnd =   .true.  !  flag to bound erp term (associated with nn_sssr=2)
+   ln_sssr_bnd =  .true.   !  flag to bound erp term (associated with nn_sssr=2)
    rn_sssr_bnd =   4.e0    !  ABS(Max/Min) value of the damping erp term [mm/day]
 /
@@ -516 +526 @@
 &namsbc_alb    !   albedo parameters
 !-----------------------------------------------------------------------
-   nn_ice_alb  =    0   !  parameterization of ice/snow albedo
-                        !     0: Shine & Henderson-Sellers (JGR 1985)
-                        !     1: "home made" based on Brandt et al. (J. Climate 2005)
-                        !                         and Grenfell & Perovich (JGR 2004)
-   rn_albice   =  0.53  !  albedo of bare puddled ice (values from 0.49 to 0.58)
-                        !     0.53 (default) => if nn_ice_alb=0
-                        !     0.50 (default) => if nn_ice_alb=1
+   nn_ice_alb  =    0      !  parameterization of ice/snow albedo
+                           !     0: Shine & Henderson-Sellers (JGR 1985)
+                           !     1: "home made" based on Brandt et al. (J. Climate 2005)
+                           !                         and Grenfell & Perovich (JGR 2004)
+   rn_albice   =  0.53     !  albedo of bare puddled ice (values from 0.49 to 0.58)
+                           !     0.53 (default) => if nn_ice_alb=0
+                           !     0.50 (default) => if nn_ice_alb=1
 /
 !-----------------------------------------------------------------------
 &namsbc_wave   ! External fields from wave model                        (ln_wave=T)
 !-----------------------------------------------------------------------
-!              !  file name  ! frequency (hours) ! variable    ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
-!              !             !  (if <0  months)  !   name      !  (logical)   !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
-   sn_cdg      =  'cdg_wave' ,        1          , 'drag_coeff',     .true.   , .false., 'daily'   ,  ''      , ''       , ''
-   sn_usd      =  'sdw_wave' ,        1          , 'u_sd2d'    ,     .true.   , .false., 'daily'   ,  ''      , ''       , ''
-   sn_vsd      =  'sdw_wave' ,        1          , 'v_sd2d'    ,     .true.   , .false., 'daily'   ,  ''      , ''       , ''
-   sn_wn       =  'sdw_wave' ,        1          , 'wave_num'  ,     .true.   , .false., 'daily'   ,  ''      , ''       , ''
+!              ! file name ! frequency (hours) ! variable    ! time interp.!  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!              !           !  (if <0  months)  !   name      !  (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
+   sn_cdg      = 'cdg_wave',        1          , 'drag_coeff',   .true.    , .false., 'daily'   ,    ''      , ''       , ''
+   sn_usd      = 'sdw_wave',        1          , 'u_sd2d'    ,   .true.    , .false., 'daily'   ,    ''      , ''       , ''
+   sn_vsd      = 'sdw_wave',        1          , 'v_sd2d'    ,   .true.    , .false., 'daily'   ,    ''      , ''       , ''
+   sn_wn       = 'sdw_wave',        1          , 'wave_num'  ,   .true.    , .false., 'daily'   ,    ''      , ''       , ''
 !
    cn_dir_cdg  = './'      !  root directory for the location of drag coefficient files
-   ln_cdgw = .false.       !  Neutral drag coefficient read from wave model
-   ln_sdw  = .false.       !  Computation of 3D stokes drift               
+   ln_cdgw     = .false.   !  Neutral drag coefficient read from wave model
+   ln_sdw      = .false.   !  Computation of 3D stokes drift               
 /
 !-----------------------------------------------------------------------
@@ -566 +576 @@
       rn_speed_limit           = 0.                   ! CFL speed limit for a berg
 
-!            ! file name ! frequency (hours) !   variable   ! time interp. !  clim   ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
-!            !           !  (if <0  months)  !     name     !   (logical)  !  (T/F ) ! 'monthly' ! filename ! pairing  ! filename      !
-      sn_icb =  'calving',       -1          , 'calvingmask',  .true.      , .true.  , 'yearly'  , ''       , ''       , ''
+!            ! file name ! frequency (hours) !   variable   ! time interp.!  clim   ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!            !           !  (if <0  months)  !     name     !  (logical)  !  (T/F ) ! 'monthly' ! filename ! pairing  ! filename      !
+      sn_icb =  'calving',       -1          , 'calvingmask',   .true.    , .true.  , 'yearly'  ,    ''    ,    ''    ,     ''
 
       cn_dir = './'
@@ -577 +587 @@
 !!======================================================================
 !!   namlbc        lateral momentum boundary condition
-!!   namobc        open boundaries parameters                           ("key_obc")
 !!   namagrif      agrif nested grid ( read by child model only )       ("key_agrif")
+!!   nam_tide      Tidal forcing 
 !!   nambdy        Unstructured open boundaries                         ("key_bdy")
-!!   namtide       Tidal forcing at open boundaries                     ("key_bdy_tides")
+!!   nambdy_dta    Unstructured open boundaries - external data         ("key_bdy")
+!!   nambdy_tide   tidal forcing at open boundaries                     ("key_bdy_tides")
 !!======================================================================
 !
@@ -602 +613 @@
 &nam_tide      !   tide parameters                                      ("key_tide")
 !-----------------------------------------------------------------------
-   ln_tide_pot   = .true.   !  use tidal potential forcing
-   ln_tide_ramp  = .false.  !
-   rdttideramp   =    0.    !
-   clname(1)     = 'DUMMY'  !  name of constituent - all tidal components must be set in namelist_cfg
+   ln_tide_pot = .true.    !  use tidal potential forcing
+   ln_tide_ramp= .false.   !
+   rdttideramp =    0.     !
+   clname(1)   = 'DUMMY'   !  name of constituent - all tidal components must be set in namelist_cfg
 /
 !-----------------------------------------------------------------------
@@ -644 +655 @@
 &nambdy_dta    !  open boundaries - external data                       ("key_bdy")
 !-----------------------------------------------------------------------
-!              !  file name      ! frequency (hours) ! variable  ! time interp. !  clim   ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
-!              !                 !  (if <0  months)  !   name    !  (logical)   !  (T/F ) ! 'monthly' ! filename ! pairing  ! filename      !
-   bn_ssh =     'amm12_bdyT_u2d' ,         24        , 'sossheig',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , ''
-   bn_u2d =     'amm12_bdyU_u2d' ,         24        , 'vobtcrtx',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , ''
-   bn_v2d =     'amm12_bdyV_u2d' ,         24        , 'vobtcrty',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , ''
-   bn_u3d  =    'amm12_bdyU_u3d' ,         24        , 'vozocrtx',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , ''
-   bn_v3d  =    'amm12_bdyV_u3d' ,         24        , 'vomecrty',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , ''
-   bn_tem  =    'amm12_bdyT_tra' ,         24        , 'votemper',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , ''
-   bn_sal  =    'amm12_bdyT_tra' ,         24        , 'vosaline',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , ''
+!              !  file name      ! frequency (hours) ! variable  ! time interp.!  clim   ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!              !                 !  (if <0  months)  !   name    !  (logical)  !  (T/F ) ! 'monthly' ! filename ! pairing  ! filename      !
+   bn_ssh      = 'amm12_bdyT_u2d',         24        , 'sossheig',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,     ''
+   bn_u2d      = 'amm12_bdyU_u2d',         24        , 'vobtcrtx',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,     ''
+   bn_v2d      = 'amm12_bdyV_u2d',         24        , 'vobtcrty',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,     ''
+   bn_u3d      = 'amm12_bdyU_u3d',         24        , 'vozocrtx',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,     ''
+   bn_v3d      = 'amm12_bdyV_u3d',         24        , 'vomecrty',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,     ''
+   bn_tem      = 'amm12_bdyT_tra',         24        , 'votemper',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,     ''
+   bn_sal      = 'amm12_bdyT_tra',         24        , 'vosaline',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,     ''
 ! for lim2
-!   bn_frld  =   'amm12_bdyT_ice' ,         24        , 'ileadfra',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , ''
-!   bn_hicif =   'amm12_bdyT_ice' ,         24        , 'iicethic',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , ''
-!   bn_hsnif =   'amm12_bdyT_ice' ,         24        , 'isnowthi',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , ''
+!   bn_frld    = 'amm12_bdyT_ice',         24        , 'ileadfra',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,     ''
+!   bn_hicif   = 'amm12_bdyT_ice',         24        , 'iicethic',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,     ''
+!   bn_hsnif   = 'amm12_bdyT_ice',         24        , 'isnowthi',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,     ''
 ! for lim3
-!   bn_a_i  =    'amm12_bdyT_ice' ,         24        , 'ileadfra',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , ''
-!   bn_ht_i =    'amm12_bdyT_ice' ,         24        , 'iicethic',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , ''
-!   bn_ht_s =    'amm12_bdyT_ice' ,         24        , 'isnowthi',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , ''
-
-   cn_dir      =    'bdydta/'   !  root directory for the location of the bulk files
-   ln_full_vel = .false.        !  
-/
-!-----------------------------------------------------------------------
-&nambdy_tide     ! tidal forcing at open boundaries
+!   bn_a_i     = 'amm12_bdyT_ice',         24        , 'ileadfra',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,     ''
+!   bn_ht_i    = 'amm12_bdyT_ice',         24        , 'iicethic',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,     ''
+!   bn_ht_s    = 'amm12_bdyT_ice',         24        , 'isnowthi',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,     ''
+
+   cn_dir      = 'bdydta/' !  root directory for the location of the bulk files
+   ln_full_vel = .false.   !  
+/
+!-----------------------------------------------------------------------
+&nambdy_tide   !  tidal forcing at open boundaries
 !-----------------------------------------------------------------------
    filtide          = 'bdydta/amm12_bdytide_'   !  file name root of tidal forcing files
@@ -672 +683 @@
    ln_bdytide_conj  = .false.                   ! 
 /
+
 !!======================================================================
 !!                 ***  Bottom boundary condition  ***
@@ -687 +699 @@
    rn_bfri1    =    4.e-4  !  bottom drag coefficient (linear case)
    rn_bfri2    =    1.e-3  !  bottom drag coefficient (non linear case). Minimum coeft if ln_loglayer=T
-   rn_bfri2_max =   1.e-1  !  max. bottom drag coefficient (non linear case and ln_loglayer=T)
+   rn_bfri2_max=    1.e-1  !  max. bottom drag coefficient (non linear case and ln_loglayer=T)
    rn_bfeb2    =    2.5e-3 !  bottom turbulent kinetic energy background  (m2/s2)
    rn_bfrz0    =    3.e-3  !  bottom roughness [m] if ln_loglayer=T
@@ -694 +706 @@
    rn_tfri1    =    4.e-4  !  top drag coefficient (linear case)
    rn_tfri2    =    2.5e-3 !  top drag coefficient (non linear case). Minimum coeft if ln_loglayer=T
-   rn_tfri2_max =   1.e-1  !  max. top drag coefficient (non linear case and ln_loglayer=T)
+   rn_tfri2_max=    1.e-1  !  max. top drag coefficient (non linear case and ln_loglayer=T)
    rn_tfeb2    =    0.0    !  top turbulent kinetic energy background  (m2/s2)
    rn_tfrz0    =    3.e-3  !  top roughness [m] if ln_loglayer=T
    ln_tfr2d    = .false.   !  horizontal variation of the top friction coef (read a 2D mask file )
-   rn_tfrien   =    50.    !  local multiplying factor of tfr (ln_tfr2d=T)
+   rn_tfrien   =   50.     !  local multiplying factor of tfr (ln_tfr2d=T)
 
    ln_bfrimp   = .true.    !  implicit bottom friction (requires ln_zdfexp = .false. if true)
@@ -720 +732 @@
 &nambbl        !   bottom boundary layer scheme                         ("key_trabbl")
 !-----------------------------------------------------------------------
-   nn_bbl_ldf  =  1      !  diffusive bbl (=1)   or not (=0)
-   nn_bbl_adv  =  0      !  advective bbl (=1/2) or not (=0)
-   rn_ahtbbl   =  1000.  !  lateral mixing coefficient in the bbl  [m2/s]
-   rn_gambbl   =  10.    !  advective bbl coefficient                 [s]
+   nn_bbl_ldf  =  1        !  diffusive bbl (=1)   or not (=0)
+   nn_bbl_adv  =  0        !  advective bbl (=1/2) or not (=0)
+   rn_ahtbbl   =  1000.    !  lateral mixing coefficient in the bbl  [m2/s]
+   rn_gambbl   =  10.      !  advective bbl coefficient                 [s]
 /
 
@@ -744 +756 @@
    ln_seos     = .false.         !  = Use simplified equation of state (S-EOS)
                                  !
-   !                     ! S-EOS coefficients :
-                                 !  rd(T,S,Z)*rau0 = -a0*(1+.5*lambda*dT+mu*Z+nu*dS)*dT+b0*dS
+   !                     ! S-EOS coefficients (ln_seos=T):
+   !                             !  rd(T,S,Z)*rau0 = -a0*(1+.5*lambda*dT+mu*Z+nu*dS)*dT+b0*dS
    rn_a0       =  1.6550e-1      !  thermal expension coefficient (nn_eos= 1)
    rn_b0       =  7.6554e-1      !  saline  expension coefficient (nn_eos= 1)
@@ -757 +769 @@
 &namtra_adv    !   advection scheme for tracer                          (default: NO advection)
 !-----------------------------------------------------------------------
-   ln_traadv_cen =  .false.  !  2nd order centered scheme
-      nn_cen_h   =  4               !  =2/4, horizontal 2nd order CEN / 4th order CEN
-      nn_cen_v   =  4               !  =2/4, vertical   2nd order CEN / 4th order COMPACT
-   ln_traadv_fct =  .false.  !  FCT scheme
-      nn_fct_h   =  2               !  =2/4, horizontal 2nd / 4th order 
-      nn_fct_v   =  2               !  =2/4, vertical   2nd / COMPACT 4th order 
-      nn_fct_zts =  0               !  >=1,  2nd order FCT scheme with vertical sub-timestepping
-      !                             !        (number of sub-timestep = nn_fct_zts)
-   ln_traadv_mus =  .false.  !  MUSCL scheme
-      ln_mus_ups =  .false.         !  use upstream scheme near river mouths
-   ln_traadv_ubs =  .false.  !  UBS scheme
-      nn_ubs_v   =  2               !  =2  , vertical 2nd order FCT / COMPACT 4th order
-   ln_traadv_qck =  .false.  !  QUICKEST scheme
+   ln_traadv_cen = .false. !  2nd order centered scheme
+      nn_cen_h   =  4            !  =2/4, horizontal 2nd order CEN / 4th order CEN
+      nn_cen_v   =  4            !  =2/4, vertical   2nd order CEN / 4th order COMPACT
+   ln_traadv_fct = .false. !  FCT scheme
+      nn_fct_h   =  2            !  =2/4, horizontal 2nd / 4th order 
+      nn_fct_v   =  2            !  =2/4, vertical   2nd / COMPACT 4th order 
+      nn_fct_zts =  0            !  >=1,  2nd order FCT scheme with vertical sub-timestepping
+      !                          !        (number of sub-timestep = nn_fct_zts)
+   ln_traadv_mus = .false. !  MUSCL scheme
+      ln_mus_ups = .false.       !  use upstream scheme near river mouths
+   ln_traadv_ubs = .false. !  UBS scheme
+      nn_ubs_v   =  2            !  =2  , vertical 2nd order FCT / COMPACT 4th order
+   ln_traadv_qck = .false. !  QUICKEST scheme
 /
 !-----------------------------------------------------------------------
 &namtra_adv_mle !   mixed layer eddy parametrisation (Fox-Kemper param) (default: NO)
 !-----------------------------------------------------------------------
-   ln_mle    = .false.      ! (T) use the Mixed Layer Eddy (MLE) parameterisation
-   rn_ce     = 0.06        ! magnitude of the MLE (typical value: 0.06 to 0.08)
-   nn_mle    = 1           ! MLE type: =0 standard Fox-Kemper ; =1 new formulation
-   rn_lf     = 5.e+3       ! typical scale of mixed layer front (meters)                      (case rn_mle=0)
-   rn_time   = 172800.     ! time scale for mixing momentum across the mixed layer (seconds)  (case rn_mle=0)
-   rn_lat    = 20.         ! reference latitude (degrees) of MLE coef.                        (case rn_mle=1)
-   nn_mld_uv = 0           ! space interpolation of MLD at u- & v-pts (0=min,1=averaged,2=max)
-   nn_conv   = 0           ! =1 no MLE in case of convection ; =0 always MLE
-   rn_rho_c_mle  = 0.01    ! delta rho criterion used to calculate MLD for FK
+   ln_mle      = .false.   ! (T) use the Mixed Layer Eddy (MLE) parameterisation
+   rn_ce       = 0.06      ! magnitude of the MLE (typical value: 0.06 to 0.08)
+   nn_mle      = 1         ! MLE type: =0 standard Fox-Kemper ; =1 new formulation
+   rn_lf       = 5.e+3     ! typical scale of mixed layer front (meters)                      (case rn_mle=0)
+   rn_time     = 172800.   ! time scale for mixing momentum across the mixed layer (seconds)  (case rn_mle=0)
+   rn_lat      = 20.       ! reference latitude (degrees) of MLE coef.                        (case rn_mle=1)
+   nn_mld_uv   = 0         ! space interpolation of MLD at u- & v-pts (0=min,1=averaged,2=max)
+   nn_conv     = 0         ! =1 no MLE in case of convection ; =0 always MLE
+   rn_rho_c_mle= 0.01      ! delta rho criterion used to calculate MLD for FK
 /
 !-----------------------------------------------------------------------
@@ -791 +803 @@
    ln_traldf_lap   =  .false.  !    laplacian operator
    ln_traldf_blp   =  .false.  !  bilaplacian operator
+   !
    !                       !  Direction of action:
    ln_traldf_lev   =  .false.  !  iso-level
@@ -866 +879 @@
    ln_vvl_layer  = .false.          !  full layer vertical coordinate
    ln_vvl_ztilde_as_zstar = .false. !  ztilde vertical coordinate emulating zstar
-   ln_vvl_zstar_at_eqtor = .false.  !  ztilde near the equator
+   ln_vvl_zstar_at_eqtor  = .false. !  ztilde near the equator
    rn_ahe3       = 0.0e0            !  thickness diffusion coefficient
    rn_rst_e3t    = 30.e0            !  ztilde to zstar restoration timescale [days]
@@ -874 +887 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_vor    !   option of physics/algorithm                          (default: NO)
+&namdyn_vor    !   Vorticity / Coriolis scheme                          (default: NO)
 !-----------------------------------------------------------------------
    ln_dynvor_ene = .false. !  enstrophy conserving scheme
@@ -953 +966 @@
    nn_havtb    =    0      !  horizontal shape for avtb (=1) or not (=0)
    ln_zdfevd   = .true.    !  enhanced vertical diffusion (evd) (T) or not (F)
-   nn_evdm     =    0      !  evd apply on tracer (=0) or on tracer and momentum (=1)
-   rn_avevd    =  100.     !  evd mixing coefficient [m2/s]
+      nn_evdm     =    0        ! evd apply on tracer (=0) or on tracer and momentum (=1)
+      rn_avevd    =  100.       !  evd mixing coefficient [m2/s]
    ln_zdfnpc   = .false.   !  Non-Penetrative Convective algorithm (T) or not (F)
-   nn_npc      =    1            !  frequency of application of npc
-   nn_npcp     =  365            !  npc control print frequency
+      nn_npc      =    1        ! frequency of application of npc
+      nn_npcp     =  365        ! npc control print frequency
    ln_zdfexp   = .false.   !  time-stepping: split-explicit (T) or implicit (F) time stepping
-   nn_zdfexp   =    3            !  number of sub-timestep for ln_zdfexp=T
+      nn_zdfexp   =    3        ! number of sub-timestep for ln_zdfexp=T
 /
 !-----------------------------------------------------------------------
 &namzdf_ric    !   richardson number dependent vertical diffusion       ("key_zdfric" )
 !-----------------------------------------------------------------------
-   rn_avmri    = 100.e-4   !  maximum value of the vertical viscosity
-   rn_alp      =   5.      !  coefficient of the parameterization
-   nn_ric      =   2       !  coefficient of the parameterization
-   rn_ekmfc    =   0.7     !  Factor in the Ekman depth Equation
-   rn_mldmin   =   1.0     !  minimum allowable mixed-layer depth estimate (m)
-   rn_mldmax   =1000.0     !  maximum allowable mixed-layer depth estimate (m)
-   rn_wtmix    =  10.0     !  vertical eddy viscosity coeff [m2/s] in the mixed-layer
-   rn_wvmix    =  10.0     !  vertical eddy diffusion coeff [m2/s] in the mixed-layer
-   ln_mldw     = .true.    !  Flag to use or not the mixed layer depth param.
+   rn_avmri    =  100.e-4  !  maximum value of the vertical viscosity
+   rn_alp      =    5.     !  coefficient of the parameterization
+   nn_ric      =    2      !  coefficient of the parameterization
+   rn_ekmfc    =    0.7    !  Factor in the Ekman depth Equation
+   rn_mldmin   =    1.0    !  minimum allowable mixed-layer depth estimate (m)
+   rn_mldmax   = 1000.0    !  maximum allowable mixed-layer depth estimate (m)
+   rn_wtmix    =   10.0    !  vertical eddy viscosity coeff [m2/s] in the mixed-layer
+   rn_wvmix    =   10.0    !  vertical eddy diffusion coeff [m2/s] in the mixed-layer
+   ln_mldw     =  .true.   !  Flag to use or not the mixed layer depth param.
 /
 !-----------------------------------------------------------------------
@@ -992 +1005 @@
    ln_lc       = .true.    !  Langmuir cell parameterisation (Axell 2002)
    rn_lc       =   0.15    !  coef. associated to Langmuir cells
-   nn_etau     =   1       !  penetration of tke below the mixed layer (ML) due to internal & intertial waves
+   nn_etau     =   1       !  penetration of tke below the mixed layer (ML) due to near intertial waves
                            !        = 0 no penetration
                            !        = 1 add a tke source below the ML
                            !        = 2 add a tke source just at the base of the ML
-                           !        = 3 as = 1 applied on HF part of the stress    ("key_oasis3")
+                           !        = 3 as = 1 applied on HF part of the stress           (ln_cpl=T)
    rn_efr      =   0.05    !  fraction of surface tke value which penetrates below the ML (nn_etau=1 or 2)
    nn_htau     =   1       !  type of exponential decrease of tke penetration below the ML
@@ -1003 +1016 @@
 /
 !-----------------------------------------------------------------------
-&namzdf_gls                !   GLS vertical diffusion                   ("key_zdfgls")
+&namzdf_gls    !   GLS vertical diffusion                               ("key_zdfgls")
 !-----------------------------------------------------------------------
    rn_emin       = 1.e-7   !  minimum value of e   [m2/s2]
@@ -1036 +1049 @@
    rn_tfe_itf  = 1.        !  ITF tidal dissipation efficiency
 /
+!-----------------------------------------------------------------------
+&namzdf_tmx_new !   internal wave-driven mixing parameterization        ("key_zdftmx_new" & "key_zdfddm")
+!-----------------------------------------------------------------------
+   nn_zpyc     = 1         !  pycnocline-intensified dissipation scales as N (=1) or N^2 (=2)
+   ln_mevar    = .true.    !  variable (T) or constant (F) mixing efficiency
+   ln_tsdiff   = .true.    !  account for differential T/S mixing (T) or not (F)
+/
+
 
 !!======================================================================
@@ -1073 +1094 @@
 /
 !-----------------------------------------------------------------------
-&namsto       ! Stochastic parametrization of EOS                       (default: NO)
-!-----------------------------------------------------------------------
-   ln_sto_eos   = .false.  ! stochastic equation of state
-   nn_sto_eos   = 1        ! number of independent random walks
-   rn_eos_stdxy = 1.4      ! random walk horz. standard deviation (in grid points)
-   rn_eos_stdz  = 0.7      ! random walk vert. standard deviation (in grid points)
-   rn_eos_tcor  = 1440.    ! random walk time correlation (in timesteps)
-   nn_eos_ord   = 1        ! order of autoregressive processes
-   nn_eos_flt   = 0        ! passes of Laplacian filter
-   rn_eos_lim   = 2.0      ! limitation factor (default = 3.0)
-   ln_rststo    = .false.  ! start from mean parameter (F) or from restart file (T)
-   ln_rstseed = .true.           ! read seed of RNG from restart file
+&namsto        ! Stochastic parametrization of EOS                      (default: NO)
+!-----------------------------------------------------------------------
+   ln_sto_eos  = .false.   ! stochastic equation of state
+   nn_sto_eos  = 1         ! number of independent random walks
+   rn_eos_stdxy= 1.4       ! random walk horz. standard deviation (in grid points)
+   rn_eos_stdz = 0.7       ! random walk vert. standard deviation (in grid points)
+   rn_eos_tcor = 1440.     ! random walk time correlation (in timesteps)
+   nn_eos_ord  = 1         ! order of autoregressive processes
+   nn_eos_flt  = 0         ! passes of Laplacian filter
+   rn_eos_lim  = 2.0       ! limitation factor (default = 3.0)
+   ln_rststo   = .false.   ! start from mean parameter (F) or from restart file (T)
+   ln_rstseed  = .true.    ! read seed of RNG from restart file
    cn_storst_in  = "restart_sto" !  suffix of stochastic parameter restart file (input)
    cn_storst_out = "restart_sto" !  suffix of stochastic parameter restart file (output)
@@ -1092 +1113 @@
 !!                  ***  Diagnostics namelists  ***
 !!======================================================================
-!!   namtrd       dynamics and/or tracer trends
-!!   namptr       Poleward Transport Diagnostics
-!!   namhsb       Heat and salt budgets
+!!   namtrd       dynamics and/or tracer trends                         (default F)
+!!   namptr       Poleward Transport Diagnostics                        (default F)
+!!   namhsb       Heat and salt budgets                                 (default F)
+!!   namdiu       Cool skin and warm layer models                       (default F)
 !!   namflo       float parameters                                      ("key_float")
-!!   nam_diaharm  Harmonic analysis of tidal constituents               ('key_diaharm')
-!!   namdct       transports through some sections
+!!   nam_diaharm  Harmonic analysis of tidal constituents               ("key_diaharm")
+!!   namdct       transports through some sections                      ("key_diadct")
+!!   nam_diatmb   Top Middle Bottom Output                              (default F)
+!!   nam_dia25h   25h Mean Output                                       (default F)
 !!   namnc4       netcdf4 chunking and compression settings             ("key_netcdf4")
 !!======================================================================
 !
 !-----------------------------------------------------------------------
-&namtrd        !   diagnostics on dynamics and/or tracer trends         (default F)
-!              !   and/or mixed-layer trends and/or barotropic vorticity
+&namtrd        !   trend diagnostics                                    (default F)
 !-----------------------------------------------------------------------
    ln_glo_trd  = .false.   ! (T) global domain averaged diag for T, T^2, KE, and PE
@@ -1123 +1146 @@
 !!gm
 !-----------------------------------------------------------------------
-&namptr       !   Poleward Transport Diagnostic                         (default F)
-!-----------------------------------------------------------------------
-   ln_diaptr  = .false.    !  Poleward heat and salt transport (T) or not (F)
-   ln_subbas  = .false.     !  Atlantic/Pacific/Indian basins computation (T) or not
-/
-!-----------------------------------------------------------------------
-&namhsb       !  Heat and salt budgets                                  (default F)
-!-----------------------------------------------------------------------
-   ln_diahsb  = .false.    !  check the heat and salt budgets (T) or not (F)
-/
-!-----------------------------------------------------------------------
-&namflo       !   float parameters                                      ("key_float")
-!-----------------------------------------------------------------------
-   jpnfl         = 1          !  total number of floats during the run
-   jpnnewflo     = 0          !  number of floats for the restart
-   ln_rstflo     = .false.    !  float restart (T) or not (F)
-   nn_writefl    =      75    !  frequency of writing in float output file
-   nn_stockfl    =    5475    !  frequency of creation of the float restart file
-   ln_argo       = .false.    !  Argo type floats (stay at the surface each 10 days)
-   ln_flork4     = .false.    !  trajectories computed with a 4th order Runge-Kutta (T)
-                              !  or computed with Blanke' scheme (F)
-   ln_ariane     = .true.     !  Input with Ariane tool convention(T)
-   ln_flo_ascii  = .true.     !  Output with Ariane tool netcdf convention(F) or ascii file (T)
-/
-!-----------------------------------------------------------------------
-&nam_diaharm   !   Harmonic analysis of tidal constituents              ('key_diaharm')
+&namptr        !   Poleward Transport Diagnostic                         (default F)
+!-----------------------------------------------------------------------
+   ln_diaptr   = .false.   !  Poleward heat and salt transport (T) or not (F)
+   ln_subbas   = .false.   !  Atlantic/Pacific/Indian basins computation (T) or not
+/
+!-----------------------------------------------------------------------
+&namhsb        !  Heat and salt budgets                                  (default F)
+!-----------------------------------------------------------------------
+   ln_diahsb   = .false.   !  check the heat and salt budgets (T) or not (F)
+/
+!-----------------------------------------------------------------------
+&namdiu        !   Cool skin and warm layer models                       (default F)
+!-----------------------------------------------------------------------
+   ln_diurnal      = .false.   ! 
+   ln_diurnal_only = .false.   !
+/
+!-----------------------------------------------------------------------
+&namflo        !   float parameters                                      ("key_float")
+!-----------------------------------------------------------------------
+   jpnfl       = 1         !  total number of floats during the run
+   jpnnewflo   = 0         !  number of floats for the restart
+   ln_rstflo   = .false.   !  float restart (T) or not (F)
+   nn_writefl  =      75   !  frequency of writing in float output file
+   nn_stockfl  =    5475   !  frequency of creation of the float restart file
+   ln_argo     = .false.   !  Argo type floats (stay at the surface each 10 days)
+   ln_flork4   = .false.   !  trajectories computed with a 4th order Runge-Kutta (T)
+   !                       !  or computed with Blanke' scheme (F)
+   ln_ariane   = .true.    !  Input with Ariane tool convention(T)
+   ln_flo_ascii= .true.    !  Output with Ariane tool netcdf convention(F) or ascii file (T)
+/
+!-----------------------------------------------------------------------
+&nam_diaharm   !   Harmonic analysis of tidal constituents               ("key_diaharm")
 !-----------------------------------------------------------------------
     nit000_han = 1         ! First time step used for harmonic analysis
@@ -1157 +1186 @@
 /
 !-----------------------------------------------------------------------
-&namdct        ! transports through some sections
-!-----------------------------------------------------------------------
-    nn_dct      = 15       !  time step frequency for transports computing
-    nn_dctwri   = 15       !  time step frequency for transports writing
-    nn_secdebug = 112      !      0 : no section to debug
-                           !     -1 : debug all section
-                           !  0 < n : debug section number n
-/
-!-----------------------------------------------------------------------
-&namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4")
+&namdct        ! transports through some sections                        ("key_diadct")
+!-----------------------------------------------------------------------
+    nn_dct     = 15        !  time step frequency for transports computing
+    nn_dctwri  = 15        !  time step frequency for transports writing
+    nn_secdebug= 112       !      0 : no section to debug
+    !                      !     -1 : debug all section
+    !                      !  0 < n : debug section number n
+/
+!-----------------------------------------------------------------------
+&nam_diatmb    !  Top Middle Bottom Output                               (default F)
+!-----------------------------------------------------------------------
+   ln_diatmb   = .false.   !  Choose Top Middle and Bottom output or not
+/
+!-----------------------------------------------------------------------
+&nam_dia25h    !  25h Mean Output                                        (default F)
+!-----------------------------------------------------------------------
+   ln_dia25h   = .false.   ! Choose 25h mean output or not
+/
+!-----------------------------------------------------------------------
+&namnc4        !   netcdf4 chunking and compression settings             ("key_netcdf4")
 !-----------------------------------------------------------------------
    nn_nchunks_i=   4       !  number of chunks in i-dimension
    nn_nchunks_j=   4       !  number of chunks in j-dimension
    nn_nchunks_k=   31      !  number of chunks in k-dimension
-                           !  setting nn_nchunks_k = jpk will give a chunk size of 1 in the vertical which
-                           !  is optimal for postprocessing which works exclusively with horizontal slabs
+   !                       !  setting nn_nchunks_k = jpk will give a chunk size of 1 in the vertical which
+   !                       !  is optimal for postprocessing which works exclusively with horizontal slabs
    ln_nc4zip   = .true.    !  (T) use netcdf4 chunking and compression
-                           !  (F) ignore chunking information and produce netcdf3-compatible files
+   !                       !  (F) ignore chunking information and produce netcdf3-compatible files
 /
 
@@ -1185 +1224 @@
 !
 !-----------------------------------------------------------------------
-&namobs       !  observation usage switch
-!-----------------------------------------------------------------------
-   ln_diaobs  = .false.             ! Logical switch for the observation operator
-   ln_t3d     = .false.             ! Logical switch for T profile observations
-   ln_s3d     = .false.             ! Logical switch for S profile observations
-   ln_sla     = .false.             ! Logical switch for SLA observations
-   ln_sst     = .false.             ! Logical switch for SST observations
-   ln_sic     = .false.             ! Logical switch for Sea Ice observations
-   ln_vel3d   = .false.             ! Logical switch for velocity observations
-   ln_altbias = .false.             ! Logical switch for altimeter bias correction
-   ln_nea     = .false.             ! Logical switch for rejection of observations near land
-   ln_grid_global = .true.          ! Logical switch for global distribution of observations
-   ln_grid_search_lookup = .false.  ! Logical switch for obs grid search w/lookup table
-   ln_ignmis  = .true.              ! Logical switch for ignoring missing files
-   ln_s_at_t  = .false.             ! Logical switch for computing model S at T obs if not there
-   ln_sstnight = .false.            ! Logical switch for calculating night-time average for SST obs
+&namobs        !  observation usage switch
+!-----------------------------------------------------------------------
+   ln_diaobs   = .false.             ! Logical switch for the observation operator
+   ln_t3d      = .false.             ! Logical switch for T profile observations
+   ln_s3d      = .false.             ! Logical switch for S profile observations
+   ln_sla      = .false.             ! Logical switch for SLA observations
+   ln_sst      = .false.             ! Logical switch for SST observations
+   ln_sic      = .false.             ! Logical switch for Sea Ice observations
+   ln_vel3d    = .false.             ! Logical switch for velocity observations
+   ln_altbias  = .false.             ! Logical switch for altimeter bias correction
+   ln_nea      = .false.             ! Logical switch for rejection of observations near land
+   ln_grid_global = .true.           ! Logical switch for global distribution of observations
+   ln_grid_search_lookup = .false.   ! Logical switch for obs grid search w/lookup table
+   ln_ignmis   = .true.              ! Logical switch for ignoring missing files
+   ln_s_at_t   = .false.             ! Logical switch for computing model S at T obs if not there
+   ln_sstnight = .false.             ! Logical switch for calculating night-time average for SST obs
 ! All of the *files* variables below are arrays. Use namelist_cfg to add more files
-   cn_profbfiles = 'profiles_01.nc'    ! Profile feedback input observation file names
-   cn_slafbfiles = 'sla_01.nc'         ! SLA feedback input observation file names
-   cn_sstfbfiles = 'sst_01.nc'         ! SST feedback input observation file names
-   cn_sicfbfiles = 'sic_01.nc'         ! SIC feedback input observation file names
-   cn_velfbfiles = 'vel_01.nc'         ! Velocity feedback input observation file names
-   cn_altbiasfile = 'altbias.nc'       ! Altimeter bias input file name
-   cn_gridsearchfile = 'gridsearch.nc' ! Grid search file name
-   rn_gridsearchres = 0.5              ! Grid search resolution
-   rn_dobsini = 00010101.000000        ! Initial date in window YYYYMMDD.HHMMSS
-   rn_dobsend = 00010102.000000        ! Final date in window YYYYMMDD.HHMMSS
-   nn_1dint = 0                        ! Type of vertical interpolation method
-   nn_2dint = 0                        ! Type of horizontal interpolation method
-   nn_msshc = 0                        ! MSSH correction scheme
-   rn_mdtcorr = 1.61                   ! MDT  correction
-   rn_mdtcutoff = 65.0                 ! MDT cutoff for computed correction
-   nn_profdavtypes = -1                ! Profile daily average types - array
-   ln_sstbias = .false. 
-   cn_sstbias_files = 'sstbias.nc'
-/
-!-----------------------------------------------------------------------
-&nam_asminc   !   assimilation increments                               ('key_asminc')
-!-----------------------------------------------------------------------
-    ln_bkgwri = .false.    !  Logical switch for writing out background state
-    ln_trainc = .false.    !  Logical switch for applying tracer increments
-    ln_dyninc = .false.    !  Logical switch for applying velocity increments
-    ln_sshinc = .false.    !  Logical switch for applying SSH increments
-    ln_asmdin = .false.    !  Logical switch for Direct Initialization (DI)
-    ln_asmiau = .false.    !  Logical switch for Incremental Analysis Updating (IAU)
-    nitbkg    = 0          !  Timestep of background in [0,nitend-nit000-1]
-    nitdin    = 0          !  Timestep of background for DI in [0,nitend-nit000-1]
-    nitiaustr = 1          !  Timestep of start of IAU interval in [0,nitend-nit000-1]
-    nitiaufin = 15         !  Timestep of end of IAU interval in [0,nitend-nit000-1]
-    niaufn    = 0          !  Type of IAU weighting function
-    ln_salfix = .false.    !  Logical switch for ensuring that the sa > salfixmin
-    salfixmin = -9999      !  Minimum salinity after applying the increments
-    nn_divdmp = 0          !  Number of iterations of divergence damping operator
-/
-!-----------------------------------------------------------------------
-&namdiu !   Cool skin and warm layer models
-!-----------------------------------------------------------------------
-   ln_diurnal      = .false.   ! 
-   ln_diurnal_only = .false.   !
-/
-!-----------------------------------------------------------------------
-&nam_diatmb  !  Top Middle Bottom Output
-!-----------------------------------------------------------------------
-   ln_diatmb  = .false.    !  Choose Top Middle and Bottom output or not
-/
-!-----------------------------------------------------------------------
-&namwad  !   Wetting and drying
-!-----------------------------------------------------------------------
-   ln_wd             = .false.  ! T/F activation of wetting and drying
-   rn_wdmin1         =  0.1     ! Minimum wet depth on dried cells
-   rn_wdmin2         =  0.01    ! Tolerance of min wet depth on dried cells
-   rn_wdld           =  20.0    ! Land elevation below which wetting/drying is allowed
-   nn_wdit           =  10      ! Max iterations for W/D limiter
-/
-!-----------------------------------------------------------------------
-&nam_dia25h  !  25h Mean Output
-!-----------------------------------------------------------------------
-   ln_dia25h  = .false.    ! Choose 25h mean output or not
-/
+   cn_profbfiles = 'profiles_01.nc'  ! Profile feedback input observation file names
+   cn_slafbfiles = 'sla_01.nc'       ! SLA feedback input observation file names
+   cn_sstfbfiles = 'sst_01.nc'       ! SST feedback input observation file names
+   cn_sicfbfiles = 'sic_01.nc'       ! SIC feedback input observation file names
+   cn_velfbfiles = 'vel_01.nc'       ! Velocity feedback input observation file names
+   cn_altbiasfile = 'altbias.nc'     ! Altimeter bias input file name
+   cn_gridsearchfile='gridsearch.nc' ! Grid search file name
+   rn_gridsearchres = 0.5            ! Grid search resolution
+   rn_dobsini  = 00010101.000000     ! Initial date in window YYYYMMDD.HHMMSS
+   rn_dobsend  = 00010102.000000     ! Final date in window YYYYMMDD.HHMMSS
+   nn_1dint    = 0                   ! Type of vertical interpolation method
+   nn_2dint    = 0                   ! Type of horizontal interpolation method
+   nn_msshc    = 0                   ! MSSH correction scheme
+   rn_mdtcorr  = 1.61                ! MDT  correction
+   rn_mdtcutoff = 65.0               ! MDT cutoff for computed correction
+   nn_profdavtypes = -1              ! Profile daily average types - array
+   ln_sstbias  = .false.             !
+   cn_sstbias_files = 'sstbias.nc'   !
+/
+!-----------------------------------------------------------------------
+&nam_asminc    !   assimilation increments                              ('key_asminc')
+!-----------------------------------------------------------------------
+    ln_bkgwri  = .false.   !  Logical switch for writing out background state
+    ln_trainc  = .false.   !  Logical switch for applying tracer increments
+    ln_dyninc  = .false.   !  Logical switch for applying velocity increments
+    ln_sshinc  = .false.   !  Logical switch for applying SSH increments
+    ln_asmdin  = .false.   !  Logical switch for Direct Initialization (DI)
+    ln_asmiau  = .false.   !  Logical switch for Incremental Analysis Updating (IAU)
+    nitbkg     = 0         !  Timestep of background in [0,nitend-nit000-1]
+    nitdin     = 0         !  Timestep of background for DI in [0,nitend-nit000-1]
+    nitiaustr  = 1         !  Timestep of start of IAU interval in [0,nitend-nit000-1]
+    nitiaufin  = 15        !  Timestep of end of IAU interval in [0,nitend-nit000-1]
+    niaufn     = 0         !  Type of IAU weighting function
+    ln_salfix  = .false.   !  Logical switch for ensuring that the sa > salfixmin
+    salfixmin  = -9999     !  Minimum salinity after applying the increments
+    nn_divdmp  = 0         !  Number of iterations of divergence damping operator
+/

trunk/NEMOGCM/NEMO/OPA_SRC/ZDF/zdfddm.F90

@@ -174 +174 @@
                   &                             +  0.15 * zrau(ji,jj)          * zmskd2(ji,jj)  )
                ! add to the eddy viscosity coef. previously computed
+# if defined key_zdftmx_new
+               ! key_zdftmx_new: New internal wave-driven param: use avs value computed by zdftmx
+               avs (ji,jj,jk) = avs(ji,jj,jk) + zavfs + zavds
+# else
                avs (ji,jj,jk) = avt(ji,jj,jk) + zavfs + zavds
+# endif
                avt (ji,jj,jk) = avt(ji,jj,jk) + zavft + zavdt
                avm (ji,jj,jk) = avm(ji,jj,jk) + MAX( zavft + zavdt, zavfs + zavds )

trunk/NEMOGCM/NEMO/OPA_SRC/ZDF/zdftke.F90

@@ -323 +323 @@
                   zwlc = zind * rn_lc * zus * SIN( rpi * gdepw_n(ji,jj,jk) / zhlc(ji,jj) )
                   !                                           ! TKE Langmuir circulation source term
-                  en(ji,jj,jk) = en(ji,jj,jk) + rdt * (1._wp - fr_i(ji,jj) ) * ( zwlc * zwlc * zwlc ) / zhlc(ji,jj) * wmask(ji,jj,jk) * tmask(ji,jj,1)
+                  en(ji,jj,jk) = en(ji,jj,jk) + rdt * (1._wp - fr_i(ji,jj) ) * ( zwlc * zwlc * zwlc )   &
+                     &                              / zhlc(ji,jj) * wmask(ji,jj,jk) * tmask(ji,jj,1)
                END DO
             END DO
@@ -375 +376 @@
             DO ji = fs_2, fs_jpim1   ! vector opt.
                zcof   = zfact1 * tmask(ji,jj,jk)
+# if defined key_zdftmx_new
+               ! key_zdftmx_new: New internal wave-driven param: set a minimum value for Kz on TKE (ensure numerical stability)
+               zzd_up = zcof * MAX( avm(ji,jj,jk+1) + avm(ji,jj,jk), 2.e-5_wp )   &  ! upper diagonal
+                  &          / (  e3t_n(ji,jj,jk  ) * e3w_n(ji,jj,jk  )  )
+               zzd_lw = zcof * MAX( avm(ji,jj,jk) + avm(ji,jj,jk-1), 2.e-5_wp )   &  ! lower diagonal
+                  &          / (  e3t_n(ji,jj,jk-1) * e3w_n(ji,jj,jk  )  )
+# else
                zzd_up = zcof * ( avm  (ji,jj,jk+1) + avm  (ji,jj,jk  ) )   &  ! upper diagonal
                   &          / ( e3t_n(ji,jj,jk  ) * e3w_n(ji,jj,jk  ) )
                zzd_lw = zcof * ( avm  (ji,jj,jk  ) + avm  (ji,jj,jk-1) )   &  ! lower diagonal
                   &          / ( e3t_n(ji,jj,jk-1) * e3w_n(ji,jj,jk  ) )
+# endif
                !                                   ! shear prod. at w-point weightened by mask
                zesh2  =  ( z3du(ji-1,jj,jk) + z3du(ji,jj,jk) ) / MAX( 1._wp , umask(ji-1,jj,jk) + umask(ji,jj,jk) )   &
@@ -732 +741 @@
       !
       ri_cri   = 2._wp    / ( 2._wp + rn_ediss / rn_ediff )   ! resulting critical Richardson number
+# if defined key_zdftmx_new
+      ! key_zdftmx_new: New internal wave-driven param: specified value of rn_emin & rmxl_min are used
+      rn_emin  = 1.e-10_wp
+      rmxl_min = 1.e-03_wp
+      IF(lwp) THEN                  ! Control print
+         WRITE(numout,*)
+         WRITE(numout,*) 'zdf_tke_init :  New tidal mixing case: force rn_emin = 1.e-10 and rmxl_min = 1.e-3 '
+         WRITE(numout,*) '~~~~~~~~~~~~'
+      ENDIF
+# else
       rmxl_min = 1.e-6_wp / ( rn_ediff * SQRT( rn_emin ) )    ! resulting minimum length to recover molecular viscosity
+# endif
       !
       IF(lwp) THEN                    !* Control print

trunk/NEMOGCM/NEMO/OPA_SRC/ZDF/zdftmx.F90

@@ -541 +541 @@
    END SUBROUTINE zdf_tmx_init
 
+#elif defined key_zdftmx_new
+   !!----------------------------------------------------------------------
+   !!   'key_zdftmx_new'               Internal wave-driven vertical mixing
+   !!----------------------------------------------------------------------
+   !!   zdf_tmx       : global     momentum & tracer Kz with wave induced Kz
+   !!   zdf_tmx_init  : global     momentum & tracer Kz with wave induced Kz
+   !!----------------------------------------------------------------------
+   USE oce            ! ocean dynamics and tracers variables
+   USE dom_oce        ! ocean space and time domain variables
+   USE zdf_oce        ! ocean vertical physics variables
+   USE zdfddm         ! ocean vertical physics: double diffusive mixing
+   USE lbclnk         ! ocean lateral boundary conditions (or mpp link)
+   USE eosbn2         ! ocean equation of state
+   USE phycst         ! physical constants
+   USE prtctl         ! Print control
+   USE in_out_manager ! I/O manager
+   USE iom            ! I/O Manager
+   USE lib_mpp        ! MPP library
+   USE wrk_nemo       ! work arrays
+   USE timing         ! Timing
+   USE lib_fortran    ! Fortran utilities (allows no signed zero when 'key_nosignedzero' defined)  
+
+   IMPLICIT NONE
+   PRIVATE
+
+   PUBLIC   zdf_tmx         ! called in step module 
+   PUBLIC   zdf_tmx_init    ! called in nemogcm module 
+   PUBLIC   zdf_tmx_alloc   ! called in nemogcm module
+
+   LOGICAL, PUBLIC, PARAMETER ::   lk_zdftmx = .TRUE.    !: wave-driven mixing flag
+
+   !                       !!* Namelist  namzdf_tmx : internal wave-driven mixing *
+   INTEGER  ::  nn_zpyc     ! pycnocline-intensified mixing energy proportional to N (=1) or N^2 (=2)
+   LOGICAL  ::  ln_mevar    ! variable (=T) or constant (=F) mixing efficiency
+   LOGICAL  ::  ln_tsdiff   ! account for differential T/S wave-driven mixing (=T) or not (=F)
+
+   REAL(wp) ::  r1_6 = 1._wp / 6._wp
+
+   REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:)   ::   ebot_tmx     ! power available from high-mode wave breaking (W/m2)
+   REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:)   ::   epyc_tmx     ! power available from low-mode, pycnocline-intensified wave breaking (W/m2)
+   REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:)   ::   ecri_tmx     ! power available from low-mode, critical slope wave breaking (W/m2)
+   REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:)   ::   hbot_tmx     ! WKB decay scale for high-mode energy dissipation (m)
+   REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:)   ::   hcri_tmx     ! decay scale for low-mode critical slope dissipation (m)
+   REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:,:) ::   emix_tmx     ! local energy density available for mixing (W/kg)
+   REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:,:) ::   bflx_tmx     ! buoyancy flux Kz * N^2 (W/kg)
+   REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:)   ::   pcmap_tmx    ! vertically integrated buoyancy flux (W/m2)
+   REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:,:) ::   zav_ratio    ! S/T diffusivity ratio (only for ln_tsdiff=T)
+   REAL(wp), ALLOCATABLE, SAVE, DIMENSION(:,:,:) ::   zav_wave     ! Internal wave-induced diffusivity
+
+   !! * Substitutions
+#  include "zdfddm_substitute.h90"
+#  include "vectopt_loop_substitute.h90"
+   !!----------------------------------------------------------------------
+   !! NEMO/OPA 4.0 , NEMO Consortium (2016)
+   !! $Id$
+   !! Software governed by the CeCILL licence     (NEMOGCM/NEMO_CeCILL.txt)
+   !!----------------------------------------------------------------------
+CONTAINS
+
+   INTEGER FUNCTION zdf_tmx_alloc()
+      !!----------------------------------------------------------------------
+      !!                ***  FUNCTION zdf_tmx_alloc  ***
+      !!----------------------------------------------------------------------
+      ALLOCATE(     ebot_tmx(jpi,jpj),  epyc_tmx(jpi,jpj),  ecri_tmx(jpi,jpj)    ,   &
+      &             hbot_tmx(jpi,jpj),  hcri_tmx(jpi,jpj),  emix_tmx(jpi,jpj,jpk),   &
+      &         bflx_tmx(jpi,jpj,jpk), pcmap_tmx(jpi,jpj), zav_ratio(jpi,jpj,jpk),   & 
+      &         zav_wave(jpi,jpj,jpk), STAT=zdf_tmx_alloc     )
+      !
+      IF( lk_mpp             )   CALL mpp_sum ( zdf_tmx_alloc )
+      IF( zdf_tmx_alloc /= 0 )   CALL ctl_warn('zdf_tmx_alloc: failed to allocate arrays')
+   END FUNCTION zdf_tmx_alloc
+
+
+   SUBROUTINE zdf_tmx( kt )
+      !!----------------------------------------------------------------------
+      !!                  ***  ROUTINE zdf_tmx  ***
+      !!                   
+      !! ** Purpose :   add to the vertical mixing coefficients the effect of
+      !!              breaking internal waves.
+      !!
+      !! ** Method  : - internal wave-driven vertical mixing is given by:
+      !!                  Kz_wave = min(  100 cm2/s, f(  Reb = emix_tmx /( Nu * N^2 )  )
+      !!              where emix_tmx is the 3D space distribution of the wave-breaking 
+      !!              energy and Nu the molecular kinematic viscosity.
+      !!              The function f(Reb) is linear (constant mixing efficiency)
+      !!              if the namelist parameter ln_mevar = F and nonlinear if ln_mevar = T.
+      !!
+      !!              - Compute emix_tmx, the 3D power density that allows to compute
+      !!              Reb and therefrom the wave-induced vertical diffusivity.
+      !!              This is divided into three components:
+      !!                 1. Bottom-intensified low-mode dissipation at critical slopes
+      !!                     emix_tmx(z) = ( ecri_tmx / rau0 ) * EXP( -(H-z)/hcri_tmx )
+      !!                                   / ( 1. - EXP( - H/hcri_tmx ) ) * hcri_tmx
+      !!              where hcri_tmx is the characteristic length scale of the bottom 
+      !!              intensification, ecri_tmx a map of available power, and H the ocean depth.
+      !!                 2. Pycnocline-intensified low-mode dissipation
+      !!                     emix_tmx(z) = ( epyc_tmx / rau0 ) * ( sqrt(rn2(z))^nn_zpyc )
+      !!                                   / SUM( sqrt(rn2(z))^nn_zpyc * e3w(z) )
+      !!              where epyc_tmx is a map of available power, and nn_zpyc
+      !!              is the chosen stratification-dependence of the internal wave
+      !!              energy dissipation.
+      !!                 3. WKB-height dependent high mode dissipation
+      !!                     emix_tmx(z) = ( ebot_tmx / rau0 ) * rn2(z) * EXP(-z_wkb(z)/hbot_tmx)
+      !!                                   / SUM( rn2(z) * EXP(-z_wkb(z)/hbot_tmx) * e3w(z) )
+      !!              where hbot_tmx is the characteristic length scale of the WKB bottom 
+      !!              intensification, ebot_tmx is a map of available power, and z_wkb is the
+      !!              WKB-stretched height above bottom defined as
+      !!                    z_wkb(z) = H * SUM( sqrt(rn2(z'>=z)) * e3w(z'>=z) )
+      !!                                 / SUM( sqrt(rn2(z'))    * e3w(z')    )
+      !!
+      !!              - update the model vertical eddy viscosity and diffusivity: 
+      !!                     avt  = avt  +    av_wave
+      !!                     avm  = avm  +    av_wave
+      !!                     avmu = avmu + mi(av_wave)
+      !!                     avmv = avmv + mj(av_wave)
+      !!
+      !!              - if namelist parameter ln_tsdiff = T, account for differential mixing:
+      !!                     avs  = avt  +    av_wave * diffusivity_ratio(Reb)
+      !!
+      !! ** Action  : - Define emix_tmx used to compute internal wave-induced mixing
+      !!              - avt, avs, avm, avmu, avmv increased by internal wave-driven mixing    
+      !!
+      !! References :  de Lavergne et al. 2015, JPO; 2016, in prep.
+      !!----------------------------------------------------------------------
+      INTEGER, INTENT(in) ::   kt   ! ocean time-step 
+      !
+      INTEGER  ::   ji, jj, jk   ! dummy loop indices
+      REAL(wp) ::   ztpc         ! scalar workspace
+      REAL(wp), DIMENSION(:,:)  , POINTER ::  zfact     ! Used for vertical structure
+      REAL(wp), DIMENSION(:,:)  , POINTER ::  zhdep     ! Ocean depth
+      REAL(wp), DIMENSION(:,:,:), POINTER ::  zwkb      ! WKB-stretched height above bottom
+      REAL(wp), DIMENSION(:,:,:), POINTER ::  zweight   ! Weight for high mode vertical distribution
+      REAL(wp), DIMENSION(:,:,:), POINTER ::  znu_t     ! Molecular kinematic viscosity (T grid)
+      REAL(wp), DIMENSION(:,:,:), POINTER ::  znu_w     ! Molecular kinematic viscosity (W grid)
+      REAL(wp), DIMENSION(:,:,:), POINTER ::  zReb      ! Turbulence intensity parameter
+      !!----------------------------------------------------------------------
+      !
+      IF( nn_timing == 1 )   CALL timing_start('zdf_tmx')
+      !
+      CALL wrk_alloc( jpi,jpj,       zfact, zhdep )
+      CALL wrk_alloc( jpi,jpj,jpk,   zwkb, zweight, znu_t, znu_w, zReb )
+
+      !                          ! ----------------------------- !
+      !                          !  Internal wave-driven mixing  !  (compute zav_wave)
+      !                          ! ----------------------------- !
+      !                             
+      !                        !* Critical slope mixing: distribute energy over the time-varying ocean depth,
+      !                                                 using an exponential decay from the seafloor.
+      DO jj = 1, jpj                ! part independent of the level
+         DO ji = 1, jpi
+            zhdep(ji,jj) = gdepw_0(ji,jj,mbkt(ji,jj)+1)       ! depth of the ocean
+            zfact(ji,jj) = rau0 * (  1._wp - EXP( -zhdep(ji,jj) / hcri_tmx(ji,jj) )  )
+            IF( zfact(ji,jj) /= 0 )   zfact(ji,jj) = ecri_tmx(ji,jj) / zfact(ji,jj)
+         END DO
+      END DO
+
+      DO jk = 2, jpkm1              ! complete with the level-dependent part
+         emix_tmx(:,:,jk) = zfact(:,:) * (  EXP( ( gde3w_n(:,:,jk  ) - zhdep(:,:) ) / hcri_tmx(:,:) )                      &
+            &                             - EXP( ( gde3w_n(:,:,jk-1) - zhdep(:,:) ) / hcri_tmx(:,:) )  ) * wmask(:,:,jk)   &
+            &                          / ( gde3w_n(:,:,jk) - gde3w_n(:,:,jk-1) )
+      END DO
+
+      !                        !* Pycnocline-intensified mixing: distribute energy over the time-varying 
+      !                        !* ocean depth as proportional to sqrt(rn2)^nn_zpyc
+
+      SELECT CASE ( nn_zpyc )
+
+      CASE ( 1 )               ! Dissipation scales as N (recommended)
+
+         zfact(:,:) = 0._wp
+         DO jk = 2, jpkm1              ! part independent of the level
+            zfact(:,:) = zfact(:,:) + e3w_n(:,:,jk) * SQRT(  MAX( 0._wp, rn2(:,:,jk) )  ) * wmask(:,:,jk)
+         END DO
+
+         DO jj = 1, jpj
+            DO ji = 1, jpi
+               IF( zfact(ji,jj) /= 0 )   zfact(ji,jj) = epyc_tmx(ji,jj) / ( rau0 * zfact(ji,jj) )
+            END DO
+         END DO
+
+         DO jk = 2, jpkm1              ! complete with the level-dependent part
+            emix_tmx(:,:,jk) = emix_tmx(:,:,jk) + zfact(:,:) * SQRT(  MAX( 0._wp, rn2(:,:,jk) )  ) * wmask(:,:,jk)
+         END DO
+
+      CASE ( 2 )               ! Dissipation scales as N^2
+
+         zfact(:,:) = 0._wp
+         DO jk = 2, jpkm1              ! part independent of the level
+            zfact(:,:) = zfact(:,:) + e3w_n(:,:,jk) * MAX( 0._wp, rn2(:,:,jk) ) * wmask(:,:,jk)
+         END DO
+
+         DO jj= 1, jpj
+            DO ji = 1, jpi
+               IF( zfact(ji,jj) /= 0 )   zfact(ji,jj) = epyc_tmx(ji,jj) / ( rau0 * zfact(ji,jj) )
+            END DO
+         END DO
+
+         DO jk = 2, jpkm1              ! complete with the level-dependent part
+            emix_tmx(:,:,jk) = emix_tmx(:,:,jk) + zfact(:,:) * MAX( 0._wp, rn2(:,:,jk) ) * wmask(:,:,jk)
+         END DO
+
+      END SELECT
+
+      !                        !* WKB-height dependent mixing: distribute energy over the time-varying 
+      !                        !* ocean depth as proportional to rn2 * exp(-z_wkb/rn_hbot)
+      
+      zwkb(:,:,:) = 0._wp
+      zfact(:,:) = 0._wp
+      DO jk = 2, jpkm1
+         zfact(:,:) = zfact(:,:) + e3w_n(:,:,jk) * SQRT(  MAX( 0._wp, rn2(:,:,jk) )  ) * wmask(:,:,jk)
+         zwkb(:,:,jk) = zfact(:,:)
+      END DO
+
+      DO jk = 2, jpkm1
+         DO jj = 1, jpj
+            DO ji = 1, jpi
+               IF( zfact(ji,jj) /= 0 )   zwkb(ji,jj,jk) = zhdep(ji,jj) * ( zfact(ji,jj) - zwkb(ji,jj,jk) )   &
+                                            &           * tmask(ji,jj,jk) / zfact(ji,jj)
+            END DO
+         END DO
+      END DO
+      zwkb(:,:,1) = zhdep(:,:) * tmask(:,:,1)
+
+      zweight(:,:,:) = 0._wp
+      DO jk = 2, jpkm1
+         zweight(:,:,jk) = MAX( 0._wp, rn2(:,:,jk) ) * hbot_tmx(:,:) * wmask(:,:,jk)                    &
+            &   * (  EXP( -zwkb(:,:,jk) / hbot_tmx(:,:) ) - EXP( -zwkb(:,:,jk-1) / hbot_tmx(:,:) )  )
+      END DO
+
+      zfact(:,:) = 0._wp
+      DO jk = 2, jpkm1              ! part independent of the level
+         zfact(:,:) = zfact(:,:) + zweight(:,:,jk)
+      END DO
+
+      DO jj = 1, jpj
+         DO ji = 1, jpi
+            IF( zfact(ji,jj) /= 0 )   zfact(ji,jj) = ebot_tmx(ji,jj) / ( rau0 * zfact(ji,jj) )
+         END DO
+      END DO
+
+      DO jk = 2, jpkm1              ! complete with the level-dependent part
+         emix_tmx(:,:,jk) = emix_tmx(:,:,jk) + zweight(:,:,jk) * zfact(:,:) * wmask(:,:,jk)   &
+            &                                / ( gde3w_n(:,:,jk) - gde3w_n(:,:,jk-1) )
+      END DO
+
+
+      ! Calculate molecular kinematic viscosity
+      znu_t(:,:,:) = 1.e-4_wp * (  17.91_wp - 0.53810_wp * tsn(:,:,:,jp_tem) + 0.00694_wp * tsn(:,:,:,jp_tem) * tsn(:,:,:,jp_tem)  &
+         &                                  + 0.02305_wp * tsn(:,:,:,jp_sal)  ) * tmask(:,:,:) * r1_rau0
+      DO jk = 2, jpkm1
+         znu_w(:,:,jk) = 0.5_wp * ( znu_t(:,:,jk-1) + znu_t(:,:,jk) ) * wmask(:,:,jk)
+      END DO
+
+      ! Calculate turbulence intensity parameter Reb
+      DO jk = 2, jpkm1
+         zReb(:,:,jk) = emix_tmx(:,:,jk) / MAX( 1.e-20_wp, znu_w(:,:,jk) * rn2(:,:,jk) )
+      END DO
+
+      ! Define internal wave-induced diffusivity
+      DO jk = 2, jpkm1
+         zav_wave(:,:,jk) = znu_w(:,:,jk) * zReb(:,:,jk) * r1_6   ! This corresponds to a constant mixing efficiency of 1/6
+      END DO
+
+      IF( ln_mevar ) THEN              ! Variable mixing efficiency case : modify zav_wave in the
+         DO jk = 2, jpkm1              ! energetic (Reb > 480) and buoyancy-controlled (Reb <10.224 ) regimes
+            DO jj = 1, jpj
+               DO ji = 1, jpi
+                  IF( zReb(ji,jj,jk) > 480.00_wp ) THEN
+                     zav_wave(ji,jj,jk) = 3.6515_wp * znu_w(ji,jj,jk) * SQRT( zReb(ji,jj,jk) )
+                  ELSEIF( zReb(ji,jj,jk) < 10.224_wp ) THEN
+                     zav_wave(ji,jj,jk) = 0.052125_wp * znu_w(ji,jj,jk) * zReb(ji,jj,jk) * SQRT( zReb(ji,jj,jk) )
+                  ENDIF
+               END DO
+            END DO
+         END DO
+      ENDIF
+
+      DO jk = 2, jpkm1                 ! Bound diffusivity by molecular value and 100 cm2/s
+         zav_wave(:,:,jk) = MIN(  MAX( 1.4e-7_wp, zav_wave(:,:,jk) ), 1.e-2_wp  ) * wmask(:,:,jk)
+      END DO
+
+      IF( kt == nit000 ) THEN        !* Control print at first time-step: diagnose the energy consumed by zav_wave
+         ztpc = 0._wp
+         DO jk = 2, jpkm1
+            DO jj = 1, jpj
+               DO ji = 1, jpi
+                  ztpc = ztpc + e3w_n(ji,jj,jk) * e1e2t(ji,jj)   &
+                     &         * MAX( 0._wp, rn2(ji,jj,jk) ) * zav_wave(ji,jj,jk) * wmask(ji,jj,jk) * tmask_i(ji,jj)
+               END DO
+            END DO
+         END DO
+         IF( lk_mpp )   CALL mpp_sum( ztpc )
+         ztpc = rau0 * ztpc ! Global integral of rauo * Kz * N^2 = power contributing to mixing 
+ 
+         IF(lwp) THEN
+            WRITE(numout,*)
+            WRITE(numout,*) 'zdf_tmx : Internal wave-driven mixing (tmx)'
+            WRITE(numout,*) '~~~~~~~ '
+            WRITE(numout,*)
+            WRITE(numout,*) '      Total power consumption by av_wave: ztpc =  ', ztpc * 1.e-12_wp, 'TW'
+         ENDIF
+      ENDIF
+
+      !                          ! ----------------------- !
+      !                          !   Update  mixing coefs  !                          
+      !                          ! ----------------------- !
+      !      
+      IF( ln_tsdiff ) THEN          !* Option for differential mixing of salinity and temperature
+         DO jk = 2, jpkm1              ! Calculate S/T diffusivity ratio as a function of Reb
+            DO jj = 1, jpj
+               DO ji = 1, jpi
+                  zav_ratio(ji,jj,jk) = ( 0.505_wp + 0.495_wp *                                                                  &
+                      &   TANH(    0.92_wp * (   LOG10(  MAX( 1.e-20_wp, zReb(ji,jj,jk) * 5._wp * r1_6 )  ) - 0.60_wp   )    )   &
+                      &                 ) * wmask(ji,jj,jk)
+               END DO
+            END DO
+         END DO
+         CALL iom_put( "av_ratio", zav_ratio )
+         DO jk = 2, jpkm1           !* update momentum & tracer diffusivity with wave-driven mixing
+            fsavs(:,:,jk) = avt(:,:,jk) + zav_wave(:,:,jk) * zav_ratio(:,:,jk)
+            avt  (:,:,jk) = avt(:,:,jk) + zav_wave(:,:,jk)
+            avm  (:,:,jk) = avm(:,:,jk) + zav_wave(:,:,jk)
+         END DO
+         !
+      ELSE                          !* update momentum & tracer diffusivity with wave-driven mixing
+         DO jk = 2, jpkm1
+            fsavs(:,:,jk) = avt(:,:,jk) + zav_wave(:,:,jk)
+            avt  (:,:,jk) = avt(:,:,jk) + zav_wave(:,:,jk)
+            avm  (:,:,jk) = avm(:,:,jk) + zav_wave(:,:,jk)
+         END DO
+      ENDIF
+
+      DO jk = 2, jpkm1              !* update momentum diffusivity at wu and wv points
+         DO jj = 2, jpjm1
+            DO ji = fs_2, fs_jpim1  ! vector opt.
+               avmu(ji,jj,jk) = avmu(ji,jj,jk) + 0.5_wp * ( zav_wave(ji,jj,jk) + zav_wave(ji+1,jj  ,jk) ) * wumask(ji,jj,jk)
+               avmv(ji,jj,jk) = avmv(ji,jj,jk) + 0.5_wp * ( zav_wave(ji,jj,jk) + zav_wave(ji  ,jj+1,jk) ) * wvmask(ji,jj,jk)
+            END DO
+         END DO
+      END DO
+      CALL lbc_lnk( avmu, 'U', 1. )   ;   CALL lbc_lnk( avmv, 'V', 1. )      ! lateral boundary condition
+
+      !                             !* output internal wave-driven mixing coefficient
+      CALL iom_put( "av_wave", zav_wave )
+                                    !* output useful diagnostics: N^2, Kz * N^2 (bflx_tmx), 
+                                    !  vertical integral of rau0 * Kz * N^2 (pcmap_tmx), energy density (emix_tmx)
+      IF( iom_use("bflx_tmx") .OR. iom_use("pcmap_tmx") ) THEN
+         bflx_tmx(:,:,:) = MAX( 0._wp, rn2(:,:,:) ) * zav_wave(:,:,:)
+         pcmap_tmx(:,:) = 0._wp
+         DO jk = 2, jpkm1
+            pcmap_tmx(:,:) = pcmap_tmx(:,:) + e3w_n(:,:,jk) * bflx_tmx(:,:,jk) * wmask(:,:,jk)
+         END DO
+         pcmap_tmx(:,:) = rau0 * pcmap_tmx(:,:)
+         CALL iom_put( "bflx_tmx", bflx_tmx )
+         CALL iom_put( "pcmap_tmx", pcmap_tmx )
+      ENDIF
+      CALL iom_put( "bn2", rn2 )
+      CALL iom_put( "emix_tmx", emix_tmx )
+      
+      CALL wrk_dealloc( jpi,jpj,       zfact, zhdep )
+      CALL wrk_dealloc( jpi,jpj,jpk,   zwkb, zweight, znu_t, znu_w, zReb )
+
+      IF(ln_ctl)   CALL prt_ctl(tab3d_1=zav_wave , clinfo1=' tmx - av_wave: ', tab3d_2=avt, clinfo2=' avt: ', ovlap=1, kdim=jpk)
+      !
+      IF( nn_timing == 1 )   CALL timing_stop('zdf_tmx')
+      !
+   END SUBROUTINE zdf_tmx
+
+
+   SUBROUTINE zdf_tmx_init
+      !!----------------------------------------------------------------------
+      !!                  ***  ROUTINE zdf_tmx_init  ***
+      !!                     
+      !! ** Purpose :   Initialization of the wave-driven vertical mixing, reading
+      !!              of input power maps and decay length scales in netcdf files.
+      !!
+      !! ** Method  : - Read the namzdf_tmx namelist and check the parameters
+      !!
+      !!              - Read the input data in NetCDF files :
+      !!              power available from high-mode wave breaking (mixing_power_bot.nc)
+      !!              power available from pycnocline-intensified wave-breaking (mixing_power_pyc.nc)
+      !!              power available from critical slope wave-breaking (mixing_power_cri.nc)
+      !!              WKB decay scale for high-mode wave-breaking (decay_scale_bot.nc)
+      !!              decay scale for critical slope wave-breaking (decay_scale_cri.nc)
+      !!
+      !! ** input   : - Namlist namzdf_tmx
+      !!              - NetCDF files : mixing_power_bot.nc, mixing_power_pyc.nc, mixing_power_cri.nc,
+      !!              decay_scale_bot.nc decay_scale_cri.nc
+      !!
+      !! ** Action  : - Increase by 1 the nstop flag is setting problem encounter
+      !!              - Define ebot_tmx, epyc_tmx, ecri_tmx, hbot_tmx, hcri_tmx
+      !!
+      !! References : de Lavergne et al. 2015, JPO; 2016, in prep.
+      !!         
+      !!----------------------------------------------------------------------
+      INTEGER  ::   ji, jj, jk   ! dummy loop indices
+      INTEGER  ::   inum         ! local integer
+      INTEGER  ::   ios
+      REAL(wp) ::   zbot, zpyc, zcri   ! local scalars
+      !!
+      NAMELIST/namzdf_tmx_new/ nn_zpyc, ln_mevar, ln_tsdiff
+      !!----------------------------------------------------------------------
+      !
+      IF( nn_timing == 1 )  CALL timing_start('zdf_tmx_init')
+      !
+      REWIND( numnam_ref )              ! Namelist namzdf_tmx in reference namelist : Wave-driven mixing
+      READ  ( numnam_ref, namzdf_tmx_new, IOSTAT = ios, ERR = 901)
+901   IF( ios /= 0 ) CALL ctl_nam ( ios , 'namzdf_tmx in reference namelist', lwp )
+      !
+      REWIND( numnam_cfg )              ! Namelist namzdf_tmx in configuration namelist : Wave-driven mixing
+      READ  ( numnam_cfg, namzdf_tmx_new, IOSTAT = ios, ERR = 902 )
+902   IF( ios /= 0 ) CALL ctl_nam ( ios , 'namzdf_tmx in configuration namelist', lwp )
+      IF(lwm) WRITE ( numond, namzdf_tmx_new )
+      !
+      IF(lwp) THEN                  ! Control print
+         WRITE(numout,*)
+         WRITE(numout,*) 'zdf_tmx_init : internal wave-driven mixing'
+         WRITE(numout,*) '~~~~~~~~~~~~'
+         WRITE(numout,*) '   Namelist namzdf_tmx_new : set wave-driven mixing parameters'
+         WRITE(numout,*) '      Pycnocline-intensified diss. scales as N (=1) or N^2 (=2) = ', nn_zpyc
+         WRITE(numout,*) '      Variable (T) or constant (F) mixing efficiency            = ', ln_mevar
+         WRITE(numout,*) '      Differential internal wave-driven mixing (T) or not (F)   = ', ln_tsdiff
+      ENDIF
+      
+      ! The new wave-driven mixing parameterization elevates avt and avm in the interior, and
+      ! ensures that avt remains larger than its molecular value (=1.4e-7). Therefore, avtb should 
+      ! be set here to a very small value, and avmb to its (uniform) molecular value (=1.4e-6).
+      avmb(:) = 1.4e-6_wp        ! viscous molecular value
+      avtb(:) = 1.e-10_wp        ! very small diffusive minimum (background avt is specified in zdf_tmx)    
+      avtb_2d(:,:) = 1.e0_wp     ! uniform 
+      IF(lwp) THEN                  ! Control print
+         WRITE(numout,*)
+         WRITE(numout,*) '   Force the background value applied to avm & avt in TKE to be everywhere ',   &
+            &               'the viscous molecular value & a very small diffusive value, resp.'
+      ENDIF
+      
+      IF( .NOT.lk_zdfddm )   CALL ctl_stop( 'STOP', 'zdf_tmx_init_new : key_zdftmx_new requires key_zdfddm' )
+      
+      !                             ! allocate tmx arrays
+      IF( zdf_tmx_alloc() /= 0 )   CALL ctl_stop( 'STOP', 'zdf_tmx_init : unable to allocate tmx arrays' )
+      !
+      !                             ! read necessary fields
+      CALL iom_open('mixing_power_bot',inum)       ! energy flux for high-mode wave breaking [W/m2]
+      CALL iom_get  (inum, jpdom_data, 'field', ebot_tmx, 1 ) 
+      CALL iom_close(inum)
+      !
+      CALL iom_open('mixing_power_pyc',inum)       ! energy flux for pynocline-intensified wave breaking [W/m2]
+      CALL iom_get  (inum, jpdom_data, 'field', epyc_tmx, 1 )
+      CALL iom_close(inum)
+      !
+      CALL iom_open('mixing_power_cri',inum)       ! energy flux for critical slope wave breaking [W/m2]
+      CALL iom_get  (inum, jpdom_data, 'field', ecri_tmx, 1 )
+      CALL iom_close(inum)
+      !
+      CALL iom_open('decay_scale_bot',inum)        ! spatially variable decay scale for high-mode wave breaking [m]
+      CALL iom_get  (inum, jpdom_data, 'field', hbot_tmx, 1 )
+      CALL iom_close(inum)
+      !
+      CALL iom_open('decay_scale_cri',inum)        ! spatially variable decay scale for critical slope wave breaking [m]
+      CALL iom_get  (inum, jpdom_data, 'field', hcri_tmx, 1 )
+      CALL iom_close(inum)
+
+      ebot_tmx(:,:) = ebot_tmx(:,:) * ssmask(:,:)
+      epyc_tmx(:,:) = epyc_tmx(:,:) * ssmask(:,:)
+      ecri_tmx(:,:) = ecri_tmx(:,:) * ssmask(:,:)
+
+      ! Set once for all to zero the first and last vertical levels of appropriate variables
+      emix_tmx (:,:, 1 ) = 0._wp
+      emix_tmx (:,:,jpk) = 0._wp
+      zav_ratio(:,:, 1 ) = 0._wp
+      zav_ratio(:,:,jpk) = 0._wp
+      zav_wave (:,:, 1 ) = 0._wp
+      zav_wave (:,:,jpk) = 0._wp
+
+      zbot = glob_sum( e1e2t(:,:) * ebot_tmx(:,:) )
+      zpyc = glob_sum( e1e2t(:,:) * epyc_tmx(:,:) )
+      zcri = glob_sum( e1e2t(:,:) * ecri_tmx(:,:) )
+      IF(lwp) THEN
+         WRITE(numout,*) '      High-mode wave-breaking energy:             ', zbot * 1.e-12_wp, 'TW'
+         WRITE(numout,*) '      Pycnocline-intensifed wave-breaking energy: ', zpyc * 1.e-12_wp, 'TW'
+         WRITE(numout,*) '      Critical slope wave-breaking energy:        ', zcri * 1.e-12_wp, 'TW'
+      ENDIF
+      !
+      IF( nn_timing == 1 )  CALL timing_stop('zdf_tmx_init')
+      !
+   END SUBROUTINE zdf_tmx_init
+
 #else
    !!----------------------------------------------------------------------