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 super-cool 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 super-cool 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 ocean-ice models.
 
-\onlyinsubfile{\input{../../global/epilogue}}
+\subinc{\input{../../global/epilogue}}
 
 \end{document}
