Index: NEMO/trunk/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex (revision 11693)
@@ 530,5 +530,5 @@
This option is described in the Report by Levier \textit{et al.} (2007), available on the \NEMO\ web site.
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/apdx_algos.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/apdx_algos.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/apdx_algos.tex (revision 11693)
@@ 311,5 +311,5 @@
\begin{figure}[!ht]
\centering
 \includegraphics[width=0.66\textwidth]{ALGOS_ISO_triad}
+ %\includegraphics[width=0.66\textwidth]{ALGOS_ISO_triad}
\caption[Triads used in the Griffies's like isoneutral diffision scheme for
$u$ and $w$components)]{
@@ 461,8 +461,7 @@
where $A_{e}$ is the eddy induced velocity coefficient,
and $r_i$ and $r_j$ the slopes between the isoneutral and the geopotential surfaces.
%%gm wrong: to be modified with 2 2D streamfunctions
+\cmtgm{Wrong: to be modified with 2 2D streamfunctions}
In other words, the eddy induced velocity can be derived from a vector streamfuntion, $\phi$,
which is given by $\phi = A_e\,\textbf{r}$ as $\textbf{U}^* = \textbf{k} \times \nabla \phi$.
%%end gm
A traditional way to implement this additional advection is to add it to the eulerian velocity prior to
@@ 822,5 +821,5 @@
\ie\ the variance of the tracer is preserved by the discretisation of the skew fluxes.
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/apdx_diff_opers.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/apdx_diff_opers.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/apdx_diff_opers.tex (revision 11693)
@@ 421,5 +421,5 @@
that is a Laplacian diffusion is applied on momentum along the coordinate directions.
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/apdx_invariants.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/apdx_invariants.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/apdx_invariants.tex (revision 11693)
@@ 25,8 +25,8 @@
\clearpage
%%% Appendix put in gmcomment as it has not been updated for \zstar and s coordinate
+%%% Appendix put in cmtgm as it has not been updated for \zstar and s coordinate
%I'm writting this appendix. It will be available in a forthcoming release of the documentation
%\gmcomment{
+%\cmtgm{
%% =================================================================================================
@@ 270,5 +270,5 @@
%gm comment
\gmcomment{
+\cmtgm{
The last equality comes from the following equation,
\begin{flalign*}
@@ 583,5 +583,5 @@
\label{subsec:INVARIANTS_2.6}
\gmcomment{
+\cmtgm{
A pressure gradient has no contribution to the evolution of the vorticity as the curl of a gradient is zero.
In the $z$coordinate, this property is satisfied locally on a Cgrid with 2nd order finite differences
@@ 694,5 +694,5 @@
%gm comment
\gmcomment{
+\cmtgm{
\begin{flalign*}
\sum\limits_{i,j,k} \biggl\{ p_t\;\partial_t b_t \biggr\} &&&\\
@@ 1479,5 +1479,5 @@
%}
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/apdx_s_coord.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/apdx_s_coord.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/apdx_s_coord.tex (revision 11693)
@@ 584,5 +584,5 @@
the expression of the 3D divergence in the $s$coordinates established above.
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/apdx_triads.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/apdx_triads.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/apdx_triads.tex (revision 11693)
@@ 1177,5 +1177,5 @@
\]
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_ASM.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_ASM.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_ASM.tex (revision 11693)
@@ 194,5 +194,5 @@
\end{clines}
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex (revision 11693)
@@ 55,5 +55,5 @@
A complete description of the use of this I/O server is presented in the next section.
%\gmcomment{ % start of gmcomment
+%\cmtgm{ % start of gmcomment
%% =================================================================================================
@@ 2061,5 +2061,5 @@
The maximum values from the run are also copied to the ocean.output file.
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIU.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIU.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIU.tex (revision 11693)
@@ 160,5 +160,5 @@
\]
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex (revision 11693)
@@ 695,5 +695,5 @@
\end{description}
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex (revision 11693)
@@ 67,6 +67,6 @@
Furthermore, the tendency terms associated with the 2D barotropic vorticity balance (when \texttt{trdvor?} is defined)
can be derived from the 3D terms.
\gmcomment{STEVEN: not quite sure I've got the sense of the last sentence. does
MISC correspond to "extracting tendency terms" or "vorticity balance"?}
+\cmtgm{STEVEN: not quite sure I've got the sense of the last sentence.
+ Does MISC correspond to "extracting tendency terms" or "vorticity balance"?}
%% =================================================================================================
@@ 153,5 +153,5 @@
as changes in the divergence of the barotropic transport are absorbed into the change of the level thicknesses,
reorientated downward.
\gmcomment{not sure of this... to be modified with the change in emp setting}
+\cmtgm{not sure of this... to be modified with the change in emp setting}
In the case of a linear free surface, the time derivative in \autoref{eq:DYN_wzv} disappears.
The upper boundary condition applies at a fixed level $z=0$.
@@ 287,5 +287,5 @@
$u$ and $v$ are located at different grid points,
a price worth paying to avoid a double averaging in the pressure gradient term as in the $B$grid.
\gmcomment{ To circumvent this, Adcroft (ADD REF HERE)
+\cmtgm{ To circumvent this, Adcroft (ADD REF HERE)
Nevertheless, this technique strongly distort the phase and group velocity of Rossby waves....}
@@ 516,5 +516,5 @@
In the vertical, the centred $2^{nd}$ order evaluation of the advection is preferred, \ie\ $u_{uw}^{ubs}$ and
$u_{vw}^{ubs}$ in \autoref{eq:DYN_adv_cen2} are used.
UBS is diffusive and is associated with vertical mixing of momentum. \gmcomment{ gm pursue the
+UBS is diffusive and is associated with vertical mixing of momentum. \cmtgm{ gm pursue the
sentence:Since vertical mixing of momentum is a source term of the TKE equation... }
@@ 534,5 +534,5 @@
there is also the possibility of using a $4^{th}$ order evaluation of the advective velocity as in ROMS.
This is an error and should be suppressed soon.
\gmcomment{action : this have to be done}
+\cmtgm{action : this have to be done}
%% =================================================================================================
@@ 915,5 +915,5 @@
it is still significant as shown by \citet{levier.treguier.ea_rpt07} in the case of an analytical barotropic Kelvin wave.
\gmcomment{ %%% copy from griffies Book
+\cmtgm{ %%% copy from griffies Book
\textbf{title: Time stepping the barotropic system }
@@ 1043,5 +1043,5 @@
%% gm %%======>>>> given here the discrete eqs provided to the solver
\gmcomment{ %%% copy from chapmodel basics
+\cmtgm{ %%% copy from chapmodel basics
\[
% \label{eq:DYN_spg_flt}
@@ 1054,5 +1054,5 @@
and $\mathrm {\mathbf M}$ represents the collected contributions of the Coriolis, hydrostatic pressure gradient,
nonlinear and viscous terms in \autoref{eq:MB_dyn}.
} %end gmcomment
+} %end cmtgm
Note that in the linear free surface formulation (\texttt{vvl?} not defined),
@@ 1082,5 +1082,5 @@
no slip or partial slip boundary conditions are applied according to the user's choice (see \autoref{chap:LBC}).
\gmcomment{
+\cmtgm{
Hyperviscous operators are frequently used in the simulation of turbulent flows to
control the dissipation of unresolved small scale features.
@@ 1183,5 +1183,5 @@
the first derivative term normal to the coast depends on the free or noslip lateral boundary conditions chosen,
while the third derivative terms normal to the coast are set to zero (see \autoref{chap:LBC}).
\gmcomment{add a remark on the the change in the position of the coefficient}
+\cmtgm{add a remark on the the change in the position of the coefficient}
%% =================================================================================================
@@ 1252,5 +1252,5 @@
the snowice mass is taken into account when computing the surface pressure gradient.
\gmcomment{ missing : the lateral boundary condition !!! another external forcing
+\cmtgm{ missing : the lateral boundary condition !!! another external forcing
}
@@ 1596,5 +1596,5 @@
and only array swapping and Asselin filtering is done in \mdl{dynnxt}.
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex (revision 11693)
@@ 25,5 +25,5 @@
\clearpage
%gm% add here introduction to this chapter
+\cmtgm{Add here introduction to this chapter}
%% =================================================================================================
@@ 708,5 +708,5 @@
direction of rotation). %, e.g. anticlockwise or clockwise.
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex (revision 11693)
@@ 68,5 +68,5 @@
\label{sec:LDF_slp}
\gmcomment{
+\cmtgm{
we should emphasize here that the implementation is a rather old one.
Better work can be achieved by using \citet{griffies.gnanadesikan.ea_JPO98, griffies_bk04} isoneutral scheme.
@@ 84,5 +84,5 @@
$r_{1f}$, $r_{1vw}$, $r_{2t}$, $r_{2vw}$ for $v$.
%gm% add here afigure of the slope in idirection
+\cmtgm{Add here afigure of the slope in idirection}
%% =================================================================================================
@@ 94,5 +94,6 @@
the diffusive fluxes in the three directions are set to zero and $T$ is assumed to be horizontally uniform,
\ie\ a linear function of $z_T$, the depth of a $T$point.
%gm { Steven : My version is obviously wrong since I'm left with an arbitrary constant which is the local vertical temperature gradient}
+\cmtgm{Steven : My version is obviously wrong since
+ I'm left with an arbitrary constant which is the local vertical temperature gradient}
\begin{equation}
@@ 112,5 +113,5 @@
\end{equation}
%gm% caution I'm not sure the simplification was a good idea!
+\cmtgm{Caution I'm not sure the simplification was a good idea!}
These slopes are computed once in \rou{ldf\_slp\_init} when \np[=.true.]{ln_sco}{ln\_sco},
@@ 144,5 +145,5 @@
\end{equation}
%gm% rewrite this as the explanation is not very clear !!!
+\cmtgm{rewrite this as the explanation is not very clear !!!}
%In practice, \autoref{eq:LDF_slp_iso} is of little help in evaluating the neutral surface slopes. Indeed, for an unsimplified equation of state, the density has a strong dependancy on pressure (here approximated as the depth), therefore applying \autoref{eq:LDF_slp_iso} using the $in situ$ density, $\rho$, computed at Tpoints leads to a flattening of slopes as the depth increases. This is due to the strong increase of the $in situ$ density with depth.
@@ 173,5 +174,4 @@
will include a pressure dependent part, leading to the wrong evaluation of the neutral slopes.
%gm%
Note: The solution for $s$coordinate passes trough the use of different (and better) expression for
the constraint on isoneutral fluxes.
@@ 182,5 +182,5 @@
\alpha \ \textbf{F}(T) = \beta \ \textbf{F}(S)
\]
 % gm{ where vector F is ....}
+ \cmtgm{where vector F is ....}
This constraint leads to the following definition for the slopes:
@@ 229,5 +229,5 @@
This allows an isoneutral diffusion scheme without additional background horizontal mixing.
This technique can be viewed as a diffusion operator that acts along largescale
(2~$\Delta$x) \gmcomment{2deltax doesnt seem very large scale} isoneutral surfaces.
+(2~$\Delta$x) \cmtgm{2deltax doesnt seem very large scale} isoneutral surfaces.
The diapycnal diffusion required for numerical stability is thus minimized and its net effect on the flow is quite small when compared to the effect of an horizontal background mixing.
@@ 478,5 +478,5 @@
%%gm from Triad appendix : to be incorporated....
\gmcomment{
+\cmtgm{
Values of isoneutral diffusivity and GM coefficient are set as described in \autoref{sec:LDF_coef}.
If none of the keys \key{traldf\_cNd}, N=1,2,3 is set (the default), spatially constant isoneutral $A_l$ and
@@ 544,5 +544,5 @@
\colorbox{yellow}{TBC}
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_OBS.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_OBS.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_OBS.tex (revision 11693)
@@ 1180,5 +1180,5 @@
\end{figure}
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex (revision 11693)
@@ 880,11 +880,29 @@
%ENDIF
%\gmcomment{ word doc of runoffs:
%In the current \NEMO\ setup river runoff is added to emp fluxes, these are then applied at just the sea surface as a volume change (in the variable volume case this is a literal volume change, and in the linear free surface case the free surface is moved) and a salt flux due to the concentration/dilution effect. There is also an option to increase vertical mixing near river mouths; this gives the effect of having a 3d river. All river runoff and emp fluxes are assumed to be fresh water (zero salinity) and at the same temperature as the sea surface.
%Our aim was to code the option to specify the temperature and salinity of river runoff, (as well as the amount), along with the depth that the river water will affect. This would make it possible to model low salinity outflow, such as the Baltic, and would allow the ocean temperature to be affected by river runoff.

%The depth option makes it possible to have the river water affecting just the surface layer, throughout depth, or some specified point in between.

%To do this we need to treat evaporation/precipitation fluxes and river runoff differently in the tra_sbc module. We decided to separate them throughout the code, so that the variable emp represented solely evaporation minus precipitation fluxes, and a new 2d variable rnf was added which represents the volume flux of river runoff (in kg/m2s to remain consistent with emp). This meant many uses of emp and emps needed to be changed, a list of all modules which use emp or emps and the changes made are below:
+\cmtgm{ word doc of runoffs:
+In the current \NEMO\ setup river runoff is added to emp fluxes,
+these are then applied at just the sea surface as a volume change (in the variable volume case
+this is a literal volume change, and in the linear free surface case the free surface is moved)
+and a salt flux due to the concentration/dilution effect.
+There is also an option to increase vertical mixing near river mouths;
+this gives the effect of having a 3d river.
+All river runoff and emp fluxes are assumed to be fresh water (zero salinity) and
+at the same temperature as the sea surface.
+Our aim was to code the option to specify the temperature and salinity of river runoff,
+(as well as the amount), along with the depth that the river water will affect.
+This would make it possible to model low salinity outflow, such as the Baltic,
+and would allow the ocean temperature to be affected by river runoff.
+
+The depth option makes it possible to have the river water affecting just the surface layer,
+throughout depth, or some specified point in between.
+
+To do this we need to treat evaporation/precipitation fluxes and river runoff differently in
+the \mdl{tra_sbc} module.
+We decided to separate them throughout the code,
+so that the variable emp represented solely evaporation minus precipitation fluxes,
+and a new 2d variable rnf was added which represents the volume flux of river runoff
+(in $kg/m^2s$ to remain consistent with $emp$).
+This meant many uses of emp and emps needed to be changed,
+a list of all modules which use $emp$ or $emps$ and the changes made are below:}
%% =================================================================================================
@@ 908,62 +926,62 @@
Two different bulk formulae are available:
 \begin{description}
 \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: The melt rate is based on a balance between the upward ocean heat flux and
 the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}.
 \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: The melt rate and the heat flux are based on a 3 equations formulation
 (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation).
 A complete description is available in \citet{jenkins_JGR91}.
 \end{description}

 Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{losch_JGR08}.
 Its thickness is defined by \np{rn_hisf_tbl}{rn\_hisf\_tbl}.
 The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the the first \np{rn_hisf_tbl}{rn\_hisf\_tbl} m.
 Then, the fluxes are spread over the same thickness (ie over one or several cells).
 If \np{rn_hisf_tbl}{rn\_hisf\_tbl} larger than top $e_{3}t$, there is no more feedback between the freezing point at the interface and the the top cell temperature.
 This can lead to supercool temperature in the top cell under melting condition.
 If \np{rn_hisf_tbl}{rn\_hisf\_tbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\

 Each melt bulk formula depends on a exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice.
 There are 3 different ways to compute the exchange coeficient:
 \begin{description}
 \item [{\np[=0]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are constant and defined by \np{rn_gammas0}{rn\_gammas0} and \np{rn_gammat0}{rn\_gammat0}.
 \begin{gather*}
+ \begin{description}
+ \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: The melt rate is based on a balance between the upward ocean heat flux and
+ the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}.
+ \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: The melt rate and the heat flux are based on a 3 equations formulation
+ (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation).
+ A complete description is available in \citet{jenkins_JGR91}.
+ \end{description}
+
+ Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{losch_JGR08}.
+ Its thickness is defined by \np{rn_hisf_tbl}{rn\_hisf\_tbl}.
+ The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the the first \np{rn_hisf_tbl}{rn\_hisf\_tbl} m.
+ Then, the fluxes are spread over the same thickness (ie over one or several cells).
+ If \np{rn_hisf_tbl}{rn\_hisf\_tbl} larger than top $e_{3}t$, there is no more feedback between the freezing point at the interface and the the top cell temperature.
+ This can lead to supercool temperature in the top cell under melting condition.
+ If \np{rn_hisf_tbl}{rn\_hisf\_tbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\
+
+ Each melt bulk formula depends on a exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice.
+ There are 3 different ways to compute the exchange coeficient:
+ \begin{description}
+ \item [{\np[=0]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are constant and defined by \np{rn_gammas0}{rn\_gammas0} and \np{rn_gammat0}{rn\_gammat0}.
+ \begin{gather*}
% \label{eq:SBC_isf_gamma_iso}
 \gamma^{T} = rn\_gammat0 \\
 \gamma^{S} = rn\_gammas0
 \end{gather*}
 This is the recommended formulation for ISOMIP.
 \item [{\np[=1]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity dependent and defined as
 \begin{gather*}
 \gamma^{T} = rn\_gammat0 \times u_{*} \\
 \gamma^{S} = rn\_gammas0 \times u_{*}
 \end{gather*}
 where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters).
 See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application.
 \item [{\np[=2]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity and stability dependent and defined as:
\[
\gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}}
\]
 where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters),
 $\Gamma_{Turb}$ the contribution of the ocean stability and
 $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion.
 See \citet{holland.jenkins_JPO99} for all the details on this formulation.
 This formulation has not been extensively tested in \NEMO\ (not recommended).
 \end{description}
 \item [{\np[=2]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented.
 The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting.
 The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL)
 (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front
 (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np[=3]{nn_isf}{nn\_isf}).
 The effective melting length (\np{sn_Leff_isf}{sn\_Leff\_isf}) is read from a file.
 \item [{\np[=3]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented.
 The fwf (\np{sn_rnfisf}{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between
 the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and
 the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}).
 The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.
 \item [{\np[=4]{nn_isf}{nn\_isf}}]: The ice shelf cavity is opened (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed).
 However, the fwf is not computed but specified from file \np{sn_fwfisf}{sn\_fwfisf}).
 The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.
 As in \np[=1]{nn_isf}{nn\_isf}, the fluxes are spread over the top boundary layer thickness (\np{rn_hisf_tbl}{rn\_hisf\_tbl})\\
+ \gamma^{T} = rn\_gammat0 \\
+ \gamma^{S} = rn\_gammas0
+ \end{gather*}
+ This is the recommended formulation for ISOMIP.
+ \item [{\np[=1]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity dependent and defined as
+ \begin{gather*}
+ \gamma^{T} = rn\_gammat0 \times u_{*} \\
+ \gamma^{S} = rn\_gammas0 \times u_{*}
+ \end{gather*}
+ where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters).
+ See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application.
+ \item [{\np[=2]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity and stability dependent and defined as:
+ \[
+ \gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}}
+ \]
+ where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters),
+ $\Gamma_{Turb}$ the contribution of the ocean stability and
+ $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion.
+ See \citet{holland.jenkins_JPO99} for all the details on this formulation.
+ This formulation has not been extensively tested in \NEMO\ (not recommended).
+ \end{description}
+\item [{\np[=2]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented.
+ The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting.
+ The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL)
+ (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front
+ (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np[=3]{nn_isf}{nn\_isf}).
+ The effective melting length (\np{sn_Leff_isf}{sn\_Leff\_isf}) is read from a file.
+\item [{\np[=3]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented.
+ The fwf (\np{sn_rnfisf}{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between
+ the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and
+ the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}).
+ The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.
+\item [{\np[=4]{nn_isf}{nn\_isf}}]: The ice shelf cavity is opened (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed).
+ However, the fwf is not computed but specified from file \np{sn_fwfisf}{sn\_fwfisf}).
+ The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.
+ As in \np[=1]{nn_isf}{nn\_isf}, the fluxes are spread over the top boundary layer thickness (\np{rn_hisf_tbl}{rn\_hisf\_tbl})
\end{description}
@@ 1521,5 +1539,5 @@
% in oceanice models.
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_STO.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_STO.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_STO.tex (revision 11693)
@@ 205,5 +205,5 @@
The first four parameters define the stochastic part of equation of state.
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex (revision 11693)
@@ 452,5 +452,5 @@
restore this property.
%%%gmcomment : Cross term are missing in the current implementation....
+\cmtgm{Cross term are missing in the current implementation....}
%% =================================================================================================
@@ 1037,5 +1037,5 @@
%!! i.e. transport proportional to the alongslope density gradient
%%%gmcomment : this section has to be really written
+\cmtgm{This section has to be really written}
When applying an advective BBL (\np[=1..2]{nn_bbl_adv}{nn\_bbl\_adv}),
@@ 1374,5 +1374,5 @@
\label{sec:TRA_zpshde}
\gmcomment{STEVEN: to be consistent with earlier discussion of differencing and averaging operators,
+\cmtgm{STEVEN: to be consistent with earlier discussion of differencing and averaging operators,
I've changed "derivative" to "difference" and "mean" to "average"}
@@ 1464,7 +1464,7 @@
Sensitivity of the advection schemes to the way horizontal averages are performed in
the vicinity of partial cells should be further investigated in the near future.
\gmcomment{gm : this last remark has to be done}

\onlyinsubfile{\input{../../global/epilogue}}
+\cmtgm{gm : this last remark has to be done}
+
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex (revision 11693)
@@ 28,5 +28,6 @@
\clearpage
%gm% Add here a small introduction to ZDF and naming of the different physics (similar to what have been written for TRA and DYN.
+\cmtgm{ Add here a small introduction to ZDF and naming of the different physics
+(similar to what have been written for TRA and DYN).}
%% =================================================================================================
@@ 1642,5 +1643,5 @@
\end{figure}
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_cfgs.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_cfgs.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_cfgs.tex (revision 11693)
@@ 292,5 +292,5 @@
Unlike ordinary river points the Baltic inputs also include salinity and temperature data.
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_conservation.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_conservation.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_conservation.tex (revision 11693)
@@ 334,5 +334,5 @@
It has not been implemented.
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex (revision 11693)
@@ 415,5 +415,5 @@
increment also applies to the time.step file which is otherwise updated every timestep.
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics.tex (revision 11693)
@@ 579,6 +579,6 @@
an explicit computation of vertical advection relative to the moving ssurfaces.
%\gmcomment{
%A key point here is that the $s$coordinate depends on $(i,j)$ ==> horizontal pressure gradient...
+\cmtgm{A key point here is that the $s$coordinate depends on $(i,j)$
+ ==> horizontal pressure gradient...}
The generalized vertical coordinates used in ocean modelling are not orthogonal,
which contrasts with many other applications in mathematical physics.
@@ 680,5 +680,5 @@
and similar expressions are used for mixing and forcing terms.
\gmcomment{
+\cmtgm{
\colorbox{yellow}{ to be updated $= = >$}
Add a few works on z and zps and s and underlies the differences between all of them
@@ 1150,5 +1150,5 @@
Nevertheless it is currently not available in the isoneutral case.
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex (revision 11693)
@@ 147,5 +147,5 @@
\begin{figure}[!t]
\centering
 \includegraphics[width=0.66\textwidth]{MBZ_DYN_dynspg_ts}
+ %\includegraphics[width=0.66\textwidth]{MBZ_DYN_dynspg_ts}
\caption[Schematic of the splitexplicit time stepping scheme for
the barotropic and baroclinic modes, after \citet{Griffies2004?}]{
@@ 311,5 +311,5 @@
In particular, this means that in filtered case, the matrix to be inverted has to be recomputed at each timestep.
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex
===================================================================
 NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex (revision 11690)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex (revision 11693)
@@ 31,5 +31,5 @@
%  daymod: definition of the time domain (nit000, nitend and the calendar)
\gmcomment{STEVEN :maybe a picture of the directory structure in the introduction which
+\cmtgm{STEVEN :maybe a picture of the directory structure in the introduction which
could be referred to here, would help ==> to be added}
@@ 158,7 +158,5 @@
\end{equation}
%%gm
%%gm UPDATE the next paragraphs with time varying thickness ...
%%gm
+\cmtgm{UPDATE the next paragraphs with time varying thickness ...}
This scheme is rather time consuming since it requires a matrix inversion.
@@ 213,5 +211,5 @@
Fast barotropic motions (such as tides) are also simulated with a better accuracy.
%\gmcomment{
+%\cmtgm{
\begin{figure}
\centering
@@ 328,5 +326,5 @@
the \nam{run}{run} namelist variables.
\gmcomment{
+\cmtgm{
add here how to force the restart to contain only one time step for operational purposes
@@ 338,5 +336,5 @@
}
\gmcomment{ % add a subsection here
+\cmtgm{ % add a subsection here
%% =================================================================================================
@@ 353,5 +351,5 @@
} %% end add
\gmcomment{ % add implicit in vvl case and CrantNicholson scheme
+\cmtgm{ % add implicit in vvl case and CrantNicholson scheme
Implicit time stepping in case of variable volume thickness.
@@ 404,5 +402,5 @@
}
\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
\end{document}