Changeset 11422 for NEMO/branches/2019/fix_vvl_ticket1791/doc/latex/NEMO/subfiles/chap_SBC.tex

Timestamp:

2019-08-08T15:40:47+02:00 (5 years ago)

Author:

jchanut

Message:

#1791, merge with trunk

Location:

NEMO/branches/2019/fix_vvl_ticket1791/doc

Files:

• . (modified) (1 prop)
• latex (modified) (1 prop)
• latex/NEMO (modified) (1 prop)
• latex/NEMO/subfiles/chap_SBC.tex (modified) (91 diffs)

NEMO/branches/2019/fix_vvl_ticket1791/doc/latex

@@ -1 @@
-*.aux
-*.bbl
-*.blg
-*.dvi
-*.fdb*
-*.fls
-*.idx
-*.ilg
-*.ind
-*.log
-*.maf
-*.mtc*
-*.out
-*.pdf
-*.toc
-_minted-*
+figures

@@ -1 @@
-*.aux
-*.bbl
-*.blg
-*.dvi
-*.fdb*
-*.fls
-*.idx
-*.ilg
-*.ind
-*.log
-*.maf
-*.mtc*
-*.out
-*.pdf
-*.toc
-_minted-*
+figures

NEMO/branches/2019/fix_vvl_ticket1791/doc/latex/NEMO/subfiles/chap_SBC.tex

@@ -2 +2 @@
 
 \begin{document}
-% ================================================================
-% Chapter —— Surface Boundary Condition (SBC, ISF, ICB) 
-% ================================================================
-\chapter{Surface Boundary Condition (SBC, ISF, ICB) }
+
+% ================================================================
+% Chapter —— Surface Boundary Condition (SBC, SAS, ISF, ICB) 
+% ================================================================
+\chapter{Surface Boundary Condition (SBC, SAS, ISF, ICB)}
 \label{chap:SBC}
 \minitoc
@@ -16 +17 @@
 %--------------------------------------------------------------------------------------------------------------
 
-The ocean needs six fields as surface boundary condition:
+The ocean needs seven fields as surface boundary condition:
+
 \begin{itemize}
 \item
@@ -26 +28 @@
 \item
   the surface salt flux associated with freezing/melting of seawater $\left( {\textit{sfx}} \right)$
+\item
+  the atmospheric pressure at the ocean surface $\left( p_a \right)$
 \end{itemize}
-plus an optional field:
+
+Four different ways are available to provide the seven fields to the ocean. They are controlled by
+namelist \ngn{namsbc} variables:
+
 \begin{itemize}
-   \item the atmospheric pressure at the ocean surface $\left( p_a \right)$
+\item
+  a bulk formulation (\np{ln\_blk}\forcode{ = .true.} with four possible bulk algorithms),
+\item
+  a flux formulation (\np{ln\_flx}\forcode{ = .true.}),
+\item
+  a coupled or mixed forced/coupled formulation (exchanges with a atmospheric model via the OASIS coupler),
+(\np{ln\_cpl} or \np{ln\_mixcpl}\forcode{ = .true.}),
+\item
+  a user defined formulation (\np{ln\_usr}\forcode{ = .true.}).
 \end{itemize}
 
-Four different ways to provide the first six fields to the ocean are available which are controlled by
-namelist \ngn{namsbc} variables:
-an analytical formulation (\np{ln\_ana}\forcode{ = .true.}),
-a flux formulation (\np{ln\_flx}\forcode{ = .true.}),
-a bulk formulae formulation (CORE (\np{ln\_blk\_core}\forcode{ = .true.}),
-CLIO (\np{ln\_blk\_clio}\forcode{ = .true.}) bulk formulae) and
-a coupled or mixed forced/coupled formulation (exchanges with a atmospheric model via the OASIS coupler)
-(\np{ln\_cpl} or \np{ln\_mixcpl}\forcode{ = .true.}). 
-When used (\ie \np{ln\_apr\_dyn}\forcode{ = .true.}),
-the atmospheric pressure forces both ocean and ice dynamics.
 
 The frequency at which the forcing fields have to be updated is given by the \np{nn\_fsbc} namelist parameter.
-When the fields are supplied from data files (flux and bulk formulations),
-the input fields need not be supplied on the model grid.
-Instead a file of coordinates and weights can be supplied which maps the data from the supplied grid to
+
+When the fields are supplied from data files (bulk, flux and mixed formulations),
+the input fields do not need to be supplied on the model grid.
+Instead, a file of coordinates and weights can be supplied to map the data from the input fields grid to
 the model points (so called "Interpolation on the Fly", see \autoref{subsec:SBC_iof}).
-If the Interpolation on the Fly option is used, input data belonging to land points (in the native grid),
-can be masked to avoid spurious results in proximity of the coasts as
+If the "Interpolation on the Fly" option is used, input data belonging to land points (in the native grid)
+should be masked or filled to avoid spurious results in proximity of the coasts, as
 large sea-land gradients characterize most of the atmospheric variables.
 
 In addition, the resulting fields can be further modified using several namelist options.
-These options control 
+These options control:
+
 \begin{itemize}
 \item
   the rotation of vector components supplied relative to an east-north coordinate system onto
-  the local grid directions in the model;
-\item
-  the addition of a surface restoring term to observed SST and/or SSS (\np{ln\_ssr}\forcode{ = .true.});
-\item
-  the modification of fluxes below ice-covered areas (using observed ice-cover or a sea-ice model)
-  (\np{nn\_ice}\forcode{ = 0..3});
-\item
-  the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np{ln\_rnf}\forcode{ = .true.});
-\item
-  the addition of isf melting as lateral inflow (parameterisation) or
-  as fluxes applied at the land-ice ocean interface (\np{ln\_isf}) ; 
+  the local grid directions in the model,
+\item
+  the use of a land/sea mask for input fields (\np{nn\_lsm}\forcode{ = .true.}),
+\item
+  the addition of a surface restoring term to observed SST and/or SSS (\np{ln\_ssr}\forcode{ = .true.}),
+\item
+  the modification of fluxes below ice-covered areas (using climatological ice-cover or a sea-ice model)
+  (\np{nn\_ice}\forcode{ = 0..3}),
+\item
+  the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np{ln\_rnf}\forcode{ = .true.}),
+\item
+  the addition of ice-shelf melting as lateral inflow (parameterisation) or
+  as fluxes applied at the land-ice ocean interface (\np{ln\_isf}\forcode{ = .true.}),
 \item
   the addition of a freshwater flux adjustment in order to avoid a mean sea-level drift
-  (\np{nn\_fwb}\forcode{ = 0..2});
-\item
-  the transformation of the solar radiation (if provided as daily mean) into a diurnal cycle
-  (\np{ln\_dm2dc}\forcode{ = .true.});
-\item
-  a neutral drag coefficient can be read from an external wave model (\np{ln\_cdgw}\forcode{ = .true.});
-\item
-  the Stokes drift rom an external wave model can be accounted (\np{ln\_sdw}\forcode{ = .true.}); 
-\item
-  the Stokes-Coriolis term can be included (\np{ln\_stcor}\forcode{ = .true.});
-\item
-  the surface stress felt by the ocean can be modified by surface waves (\np{ln\_tauwoc}\forcode{ = .true.}).
+  (\np{nn\_fwb}\forcode{ = 0..2}),
+\item
+  the transformation of the solar radiation (if provided as daily mean) into an analytical diurnal cycle
+  (\np{ln\_dm2dc}\forcode{ = .true.}),
+\item
+  the activation of wave effects from an external wave model  (\np{ln\_wave}\forcode{ = .true.}),
+\item
+  a neutral drag coefficient is read from an external wave model (\np{ln\_cdgw}\forcode{ = .true.}),
+\item
+  the Stokes drift from an external wave model is accounted for (\np{ln\_sdw}\forcode{ = .true.}), 
+\item
+  the choice of the Stokes drift profile parameterization (\np{nn\_sdrift}\forcode{ = 0..2}), 
+\item
+  the surface stress given to the ocean is modified by surface waves (\np{ln\_tauwoc}\forcode{ = .true.}),
+\item
+  the surface stress given to the ocean is read from an external wave model (\np{ln\_tauw}\forcode{ = .true.}),
+\item
+  the Stokes-Coriolis term is included (\np{ln\_stcor}\forcode{ = .true.}),
+\item
+  the light penetration in the ocean (\np{ln\_traqsr}\forcode{ = .true.} with namelist \ngn{namtra\_qsr}),
+\item
+  the atmospheric surface pressure gradient effect on ocean and ice dynamics (\np{ln\_apr\_dyn}\forcode{ = .true.} with namelist \ngn{namsbc\_apr}),
+\item
+  the effect of sea-ice pressure on the ocean (\np{ln\_ice\_embd}\forcode{ = .true.}).
 \end{itemize}
 
-In this chapter, we first discuss where the surface boundary condition appears in the model equations.
-Then we present the five ways of providing the surface boundary condition, 
+In this chapter, we first discuss where the surface boundary conditions appear in the model equations.
+Then we present the three ways of providing the surface boundary conditions, 
 followed by the description of the atmospheric pressure and the river runoff. 
-Next the scheme for interpolation on the fly is described.
+Next, the scheme for interpolation on the fly is described.
 Finally, the different options that further modify the fluxes applied to the ocean are discussed.
 One of these is modification by icebergs (see \autoref{sec:ICB_icebergs}),
@@ -95 +116 @@
 
 
+
 % ================================================================
 % Surface boundary condition for the ocean
 % ================================================================
 \section{Surface boundary condition for the ocean}
-\label{sec:SBC_general}
+\label{sec:SBC_ocean}
 
 The surface ocean stress is the stress exerted by the wind and the sea-ice on the ocean.
@@ -111 +133 @@
 The former is the non penetrative part of the heat flux
 (\ie the sum of sensible, latent and long wave heat fluxes plus
-the heat content of the mass exchange with the atmosphere and sea-ice).
+the heat content of the mass exchange between the ocean and sea-ice).
 It is applied in \mdl{trasbc} module as a surface boundary condition trend of
 the first level temperature time evolution equation
-(see \autoref{eq:tra_sbc} and \autoref{eq:tra_sbc_lin} in \autoref{subsec:TRA_sbc}). 
+(see \autoref{eq:tra_sbc} and \autoref{eq:tra_sbc_lin} in \autoref{subsec:TRA_sbc}).
 The latter is the penetrative part of the heat flux.
-It is applied as a 3D trends of the temperature equation (\mdl{traqsr} module) when
+It is applied as a 3D trend of the temperature equation (\mdl{traqsr} module) when
 \np{ln\_traqsr}\forcode{ = .true.}.
 The way the light penetrates inside the water column is generally a sum of decreasing exponentials
@@ -124 +146 @@
 It represents the mass flux exchanged with the atmosphere (evaporation minus precipitation) and
 possibly with the sea-ice and ice shelves (freezing minus melting of ice).
-It affects both the ocean in two different ways:
-$(i)$  it changes the volume of the ocean and therefore appears in the sea surface height equation as
+It affects the ocean in two different ways:
+$(i)$  it changes the volume of the ocean, and therefore appears in the sea surface height equation as      %GS: autoref ssh equation to be added
 a volume flux, and 
 $(ii)$ it changes the surface temperature and salinity through the heat and salt contents of
-the mass exchanged with the atmosphere, the sea-ice and the ice shelves. 
+the mass exchanged with atmosphere, sea-ice and ice shelves.
 
 
@@ -157 +179 @@
 the surface currents, temperature and salinity.  
 These variables are averaged over \np{nn\_fsbc} time-step (\autoref{tab:ssm}), and
-it is these averaged fields which are used to computes the surface fluxes at a frequency of \np{nn\_fsbc} time-step.
+these averaged fields are used to compute the surface fluxes at the frequency of \np{nn\_fsbc} time-steps.
 
 
@@ -165 +187 @@
     \begin{tabular}{|l|l|l|l|}
       \hline
-      Variable description             & Model variable  & Units  & point \\  \hline
-      i-component of the surface current  & ssu\_m & $m.s^{-1}$   & U \\   \hline
-      j-component of the surface current  & ssv\_m & $m.s^{-1}$   & V \\   \hline
-      Sea surface temperature          & sst\_m & \r{}$K$      & T \\   \hline
-      Sea surface salinty              & sss\_m & $psu$        & T \\   \hline
+      Variable description                         & Model variable  & Units  & point                 \\\hline
+      i-component of the surface current  & ssu\_m               & $m.s^{-1}$     & U     \\\hline
+      j-component of the surface current  & ssv\_m               & $m.s^{-1}$     & V     \\ \hline
+      Sea surface temperature                & sst\_m               & \r{}$K$              & T     \\\hline
+      Sea surface salinty                          & sss\_m               & $psu$              & T     \\   \hline
     \end{tabular}
     \caption{
       \protect\label{tab:ssm}
       Ocean variables provided by the ocean to the surface module (SBC).
-      The variable are averaged over nn{\_}fsbc time step,
+      The variable are averaged over \np{nn\_fsbc} time-step,
       \ie the frequency of computation of surface fluxes.
     }
@@ -184 +206 @@
 
 
+
 % ================================================================
 %       Input Data 
@@ -191 +214 @@
 
 A generic interface has been introduced to manage the way input data
-(2D or 3D fields, like surface forcing or ocean T and S) are specify in \NEMO.
-This task is archieved by \mdl{fldread}.
-The module was design with four main objectives in mind: 
+(2D or 3D fields, like surface forcing or ocean T and S) are specified in \NEMO.
+This task is achieved by \mdl{fldread}.
+The module is designed with four main objectives in mind: 
 \begin{enumerate}
 \item
-  optionally provide a time interpolation of the input data at model time-step, whatever their input frequency is,
+  optionally provide a time interpolation of the input data every specified model time-step, whatever their input frequency is,
   and according to the different calendars available in the model.
 \item
@@ -204 +227 @@
 \item
   provide a simple user interface and a rather simple developer interface by
-  limiting the number of prerequisite information. 
-\end{enumerate}  
-
-As a results the user have only to fill in for each variable a structure in the namelist file to
+  limiting the number of prerequisite informations. 
+\end{enumerate}
+
+As a result, the user has only to fill in for each variable a structure in the namelist file to
 define the input data file and variable names, the frequency of the data (in hours or months),
 whether its is climatological data or not, the period covered by the input file (one year, month, week or day),
-and three additional parameters for on-the-fly interpolation.
+and three additional parameters for the on-the-fly interpolation.
 When adding a new input variable, the developer has to add the associated structure in the namelist,
 read this information by mirroring the namelist read in \rou{sbc\_blk\_init} for example,
@@ -220 +243 @@
 
 Note that when an input data is archived on a disc which is accessible directly from the workspace where
-the code is executed, then the use can set the \np{cn\_dir} to the pathway leading to the data.
-By default, the data are assumed to have been copied so that cn\_dir='./'.
+the code is executed, then the user can set the \np{cn\_dir} to the pathway leading to the data.
+By default, the data are assumed to be in the same directory as the executable, so that cn\_dir='./'.
+
 
 % -------------------------------------------------------------------------------------------------------------
 % Input Data specification (\mdl{fldread})
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Input data specification (\protect\mdl{fldread})}
+\subsection[Input data specification (\textit{fldread.F90})]
+{Input data specification (\protect\mdl{fldread})}
 \label{subsec:SBC_fldread}
 
@@ -237 +262 @@
 \begin{description}  
 \item[File name]:
-  the stem name of the NetCDF file to be open.
+  the stem name of the NetCDF file to be opened.
   This stem will be completed automatically by the model, with the addition of a '.nc' at its end and
   by date information and possibly a prefix (when using AGRIF).
@@ -248 +273 @@
       \begin{tabular}{|l|c|c|c|}
         \hline
-        & daily or weekLLL         & monthly                   &   yearly          \\   \hline
-        \np{clim}\forcode{ = .false.}  & fn\_yYYYYmMMdDD.nc  &   fn\_yYYYYmMM.nc   &   fn\_yYYYY.nc  \\   \hline
-        \np{clim}\forcode{ = .true.}         & not possible                  &  fn\_m??.nc             &   fn                \\   \hline
+                                        &  daily or weekLL     &  monthly           &  yearly        \\   \hline
+        \np{clim}\forcode{ = .false.}  &  fn\_yYYYYmMMdDD.nc  &  fn\_yYYYYmMM.nc   &  fn\_yYYYY.nc  \\   \hline
+        \np{clim}\forcode{ = .true.}   &  not possible        &  fn\_m??.nc        &  fn            \\   \hline
       \end{tabular}
     \end{center}
     \caption{
       \protect\label{tab:fldread}
-      naming nomenclature for climatological or interannual input file, as a function of the Open/close frequency.
+      naming nomenclature for climatological or interannual input file(s), as a function of the open/close frequency.
       The stem name is assumed to be 'fn'.
       For weekly files, the 'LLL' corresponds to the first three letters of the first day of the week
@@ -262 +287 @@
       Note that (1) in mpp, if the file is split over each subdomain, the suffix '.nc' is replaced by '\_PPPP.nc',
       where 'PPPP' is the process number coded with 4 digits;
-      (2) when using AGRIF, the prefix '\_N' is added to files, where 'N'  is the child grid number.
+      (2) when using AGRIF, the prefix '\_N' is added to files, where 'N' is the child grid number.
     }
   \end{table}
@@ -272 +297 @@
   Its unit is in hours if it is positive (for example 24 for daily forcing) or in months if negative
   (for example -1 for monthly forcing or -12 for annual forcing).
-  Note that this frequency must really be an integer and not a real.
-  On some computers, seting it to '24.' can be interpreted as 240!
+  Note that this frequency must REALLY be an integer and not a real.
+  On some computers, setting it to '24.' can be interpreted as 240!
 
 \item[Variable name]:
@@ -284 +309 @@
   00h00'00'' to 23h59'59".
   If set to 'true', the forcing will have a broken line shape.
-  Records are assumed to be dated the middle of the forcing period.
+  Records are assumed to be dated at the middle of the forcing period.
   For example, when using a daily forcing with time interpolation,
   linear interpolation will be performed between mid-day of two consecutive days. 
@@ -291 +316 @@
   a logical to specify if a input file contains climatological forcing which can be cycle in time,
   or an interannual forcing which will requires additional files if
-  the period covered by the simulation exceed the one of the file.
-  See the above the file naming strategy which impacts the expected name of the file to be opened. 
+  the period covered by the simulation exceeds the one of the file.
+  See the above file naming strategy which impacts the expected name of the file to be opened. 
 
 \item[Open/close frequency]:
@@ -301 +326 @@
   Files are assumed to contain data from the beginning of the open/close period.
   For example, the first record of a yearly file containing daily data is Jan 1st even if
-  the experiment is not starting at the beginning of the year. 
+  the experiment is not starting at the beginning of the year.
 
 \item[Others]:
@@ -313 +338 @@
 The only tricky point is therefore to specify the date at which we need to do the interpolation and
 the date of the records read in the input files.
-Following \citet{Leclair_Madec_OM09}, the date of a time step is set at the middle of the time step.
-For example, for an experiment starting at 0h00'00" with a one hour time-step,
+Following \citet{leclair.madec_OM09}, the date of a time step is set at the middle of the time step.
+For example, for an experiment starting at 0h00'00" with a one-hour time-step,
 a time interpolation will be performed at the following time: 0h30'00", 1h30'00", 2h30'00", etc.
 However, for forcing data related to the surface module,
 values are not needed at every time-step but at every \np{nn\_fsbc} time-step.
 For example with \np{nn\_fsbc}\forcode{ = 3}, the surface module will be called at time-steps 1, 4, 7, etc.
-The date used for the time interpolation is thus redefined to be at the middle of \np{nn\_fsbc} time-step period.
+The date used for the time interpolation is thus redefined to the middle of \np{nn\_fsbc} time-step period.
 In the previous example, this leads to: 1h30'00", 4h30'00", 7h30'00", etc. \\ 
 (2) For code readablility and maintenance issues, we don't take into account the NetCDF input file calendar.
@@ -325 +350 @@
 user in the record frequency, the open/close frequency and the type of temporal interpolation.
 For example, the first record of a yearly file containing daily data that will be interpolated in time is assumed to
-be start Jan 1st at 12h00'00" and end Dec 31st at 12h00'00". \\
+start Jan 1st at 12h00'00" and end Dec 31st at 12h00'00". \\
 (3) If a time interpolation is requested, the code will pick up the needed data in the previous (next) file when
 interpolating data with the first (last) record of the open/close period.
@@ -333 +358 @@
 If the forcing is climatological, Dec and Jan will be keep-up from the same year.
 However, if the forcing is not climatological, at the end of
-the open/close period the code will automatically close the current file and open the next one.
+the open/close period, the code will automatically close the current file and open the next one.
 Note that, if the experiment is starting (ending) at the beginning (end) of
-an open/close period we do accept that the previous (next) file is not existing.
+an open/close period, we do accept that the previous (next) file is not existing.
 In this case, the time interpolation will be performed between two identical values.
 For example, when starting an experiment on Jan 1st of year Y with yearly files and daily data to be interpolated,
@@ -353 +378 @@
 Interpolation on the Fly allows the user to supply input files required for the surface forcing on
 grids other than the model grid.
-To do this he or she must supply, in addition to the source data file, a file of weights to be used to
+To do this, he or she must supply, in addition to the source data file(s), a file of weights to be used to
 interpolate from the data grid to the model grid.
 The original development of this code used the SCRIP package
 (freely available \href{http://climate.lanl.gov/Software/SCRIP}{here} under a copyright agreement).
-In principle, any package can be used to generate the weights, but the variables in
+In principle, any package such as CDO can be used to generate the weights, but the variables in
 the input weights file must have the same names and meanings as assumed by the model.
-Two methods are currently available: bilinear and bicubic interpolation.
+Two methods are currently available: bilinear and bicubic interpolations.
 Prior to the interpolation, providing a land/sea mask file, the user can decide to remove land points from
 the input file and substitute the corresponding values with the average of the 8 neighbouring points in
@@ -365 +390 @@
 Only "sea points" are considered for the averaging.
 The land/sea mask file must be provided in the structure associated with the input variable.
-The netcdf land/sea mask variable name must be 'LSM' it must have the same horizontal and vertical dimensions of
-the associated variable and should be equal to 1 over land and 0 elsewhere.
-The procedure can be recursively applied setting nn\_lsm > 1 in namsbc namelist.
-Note that nn\_lsm=0 forces the code to not apply the procedure even if a file for land/sea mask is supplied.
-
+The netcdf land/sea mask variable name must be 'LSM' and must have the same horizontal and vertical dimensions as
+the associated variables and should be equal to 1 over land and 0 elsewhere.
+The procedure can be recursively applied by setting nn\_lsm > 1 in namsbc namelist.
+Note that nn\_lsm=0 forces the code to not apply the procedure, even if a land/sea mask file is supplied.
+
+
+% -------------------------------------------------------------------------------------------------------------
+% Bilinear interpolation
+% -------------------------------------------------------------------------------------------------------------
 \subsubsection{Bilinear interpolation}
 \label{subsec:SBC_iof_bilinear}
@@ -375 +404 @@
 The input weights file in this case has two sets of variables:
 src01, src02, src03, src04 and wgt01, wgt02, wgt03, wgt04.
-The "src" variables correspond to the point in the input grid to which the weight "wgt" is to be applied.
+The "src" variables correspond to the point in the input grid to which the weight "wgt" is applied.
 Each src value is an integer corresponding to the index of a point in the input grid when
 written as a one dimensional array.
@@ -391 +420 @@
 and wgt(1) corresponds to variable "wgt01" for example.
 
+
+% -------------------------------------------------------------------------------------------------------------
+% Bicubic interpolation
+% -------------------------------------------------------------------------------------------------------------
 \subsubsection{Bicubic interpolation}
 \label{subsec:SBC_iof_bicubic}
 
-Again there are two sets of variables: "src" and "wgt".
-But in this case there are 16 of each.
+Again, there are two sets of variables: "src" and "wgt".
+But in this case, there are 16 of each.
 The symbolic algorithm used to calculate values on the model grid is now:
 
@@ -401 +434 @@
   \begin{split}
     f_{m}(i,j) =  f_{m}(i,j) +& \sum_{k=1}^{4} {wgt(k)f(idx(src(k)))}
-    +   \sum_{k=5}^{8} {wgt(k)\left.\frac{\partial f}{\partial i}\right| _{idx(src(k))} }    \\
-    +& \sum_{k=9}^{12} {wgt(k)\left.\frac{\partial f}{\partial j}\right| _{idx(src(k))} }
-    +   \sum_{k=13}^{16} {wgt(k)\left.\frac{\partial ^2 f}{\partial i \partial j}\right| _{idx(src(k))} }
+    +  \sum_{k=5 }^{8 } {wgt(k)\left.\frac{\partial f}{\partial i}\right| _{idx(src(k))} }    \\
+    +& \sum_{k=9 }^{12} {wgt(k)\left.\frac{\partial f}{\partial j}\right| _{idx(src(k))} }
+    +  \sum_{k=13}^{16} {wgt(k)\left.\frac{\partial ^2 f}{\partial i \partial j}\right| _{idx(src(k))} }
   \end{split}
 \]
 The gradients here are taken with respect to the horizontal indices and not distances since
-the spatial dependency has been absorbed into the weights.
-
+the spatial dependency has been included into the weights.
+
+
+% -------------------------------------------------------------------------------------------------------------
+% Implementation
+% -------------------------------------------------------------------------------------------------------------
 \subsubsection{Implementation}
 \label{subsec:SBC_iof_imp}
@@ -420 +457 @@
 inspecting a global attribute stored in the weights input file.
 This attribute must be called "ew\_wrap" and be of integer type.
-If it is negative, the input non-model grid is assumed not to be cyclic.
+If it is negative, the input non-model grid is assumed to be not cyclic.
 If zero or greater, then the value represents the number of columns that overlap.
 $E.g.$ if the input grid has columns at longitudes 0, 1, 2, .... , 359, then ew\_wrap should be set to 0;
 if longitudes are 0.5, 2.5, .... , 358.5, 360.5, 362.5, ew\_wrap should be 2.
 If the model does not find attribute ew\_wrap, then a value of -999 is assumed.
-In this case the \rou{fld\_read} routine defaults ew\_wrap to value 0 and
+In this case, the \rou{fld\_read} routine defaults ew\_wrap to value 0 and
 therefore the grid is assumed to be cyclic with no overlapping columns.
-(In fact this only matters when bicubic interpolation is required.)
+(In fact, this only matters when bicubic interpolation is required.)
 Note that no testing is done to check the validity in the model,
 since there is no way of knowing the name used for the longitude variable,
@@ -444 +481 @@
 or is a copy of one from the first few columns on the opposite side of the grid (cyclical case).
 
+
+% -------------------------------------------------------------------------------------------------------------
+% Limitations
+% -------------------------------------------------------------------------------------------------------------
 \subsubsection{Limitations}
 \label{subsec:SBC_iof_lim}
@@ -449 +490 @@
 \begin{enumerate}  
 \item
-  The case where input data grids are not logically rectangular has not been tested.
+  The case where input data grids are not logically rectangular (irregular grid case) has not been tested.
 \item
   This code is not guaranteed to produce positive definite answers from positive definite inputs when
@@ -470 +511 @@
 (see the directory NEMOGCM/TOOLS/WEIGHTS).
 
+
 % -------------------------------------------------------------------------------------------------------------
 % Standalone Surface Boundary Condition Scheme
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Standalone surface boundary condition scheme}
-\label{subsec:SAS_iof}
-
-%---------------------------------------namsbc_ana--------------------------------------------------
+\subsection{Standalone surface boundary condition scheme (SAS)}
+\label{subsec:SAS}
+
+%---------------------------------------namsbc_sas--------------------------------------------------
 
 \nlst{namsbc_sas}
 %--------------------------------------------------------------------------------------------------------------
 
-In some circumstances it may be useful to avoid calculating the 3D temperature,
+In some circumstances, it may be useful to avoid calculating the 3D temperature,
 salinity and velocity fields and simply read them in from a previous run or receive them from OASIS.  
 For example:
@@ -496 +538 @@
   Spinup of the iceberg floats
 \item
-  Ocean/sea-ice simulation with both media running in parallel (\np{ln\_mixcpl}\forcode{ = .true.})
+  Ocean/sea-ice simulation with both models running in parallel (\np{ln\_mixcpl}\forcode{ = .true.})
 \end{itemize}
 
-The StandAlone Surface scheme provides this utility.
+The Standalone Surface scheme provides this capacity.
 Its options are defined through the \ngn{namsbc\_sas} namelist variables.
 A new copy of the model has to be compiled with a configuration based on ORCA2\_SAS\_LIM.
-However no namelist parameters need be changed from the settings of the previous run (except perhaps nn{\_}date0).
+However, no namelist parameters need be changed from the settings of the previous run (except perhaps nn{\_}date0).
 In this configuration, a few routines in the standard model are overriden by new versions.
 Routines replaced are:
@@ -524 +566 @@
   so calls to restart functions have been removed.
   This also means that the calendar cannot be controlled by time in a restart file,
-  so the user must make sure that nn{\_}date0 in the model namelist is correct for his or her purposes.
+  so the user must check that nn{\_}date0 in the model namelist is correct for his or her purposes.
 \item
   \mdl{stpctl}:
@@ -543 +585 @@
   velocity arrays at the surface.
   These filenames are supplied in namelist namsbc{\_}sas.
-  Unfortunately because of limitations with the \mdl{iom} module,
+  Unfortunately, because of limitations with the \mdl{iom} module,
   the full 3D fields from the mean files have to be read in and interpolated in time,
   before using just the top level.
@@ -550 +592 @@
 
 
-% Missing the description of the 2 following variables:
-%   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
-
-
-
-% ================================================================
-% Analytical formulation (sbcana module) 
-% ================================================================
-\section{Analytical formulation (\protect\mdl{sbcana})}
-\label{sec:SBC_ana}
-
-%---------------------------------------namsbc_ana--------------------------------------------------
-%
-%\nlst{namsbc_ana}
-%--------------------------------------------------------------------------------------------------------------
-
-The analytical formulation of the surface boundary condition is the default scheme.
-In this case, all the six fluxes needed by the ocean are assumed to be uniform in space.
-They take constant values given in the namelist \ngn{namsbc{\_}ana} by
-the variables \np{rn\_utau0}, \np{rn\_vtau0}, \np{rn\_qns0}, \np{rn\_qsr0}, and \np{rn\_emp0}
-($\textit{emp}=\textit{emp}_S$).
-The runoff is set to zero.
-In addition, the wind is allowed to reach its nominal value within a given number of time steps (\np{nn\_tau000}).
-
-If a user wants to apply a different analytical forcing,
-the \mdl{sbcana} module can be modified to use another scheme.
-As an example, the \mdl{sbc\_ana\_gyre} routine provides the analytical forcing for the GYRE configuration
-(see GYRE configuration manual, in preparation).
+The user can also choose in the \ngn{namsbc\_sas} namelist to read the mean (nn\_fsbc time-step) fraction of solar net radiation absorbed in the 1st T level using
+ (\np{ln\_flx}\forcode{ = .true.}) and to provide 3D oceanic velocities instead of 2D ones (\np{ln\_flx}\forcode{ = .true.}). In that last case, only the 1st level will be read in.
+
 
 
@@ -584 +600 @@
 % Flux formulation 
 % ================================================================
-\section{Flux formulation (\protect\mdl{sbcflx})}
+\section[Flux formulation (\textit{sbcflx.F90})]
+{Flux formulation (\protect\mdl{sbcflx})}
 \label{sec:SBC_flx}
 %------------------------------------------namsbc_flx----------------------------------------------------
@@ -602 +619 @@
 
 
+
 % ================================================================
 % Bulk formulation
 % ================================================================
-\section[Bulk formulation {(\textit{sbcblk\{\_core,\_clio\}.F90})}]
-                        {Bulk formulation {(\protect\mdl{sbcblk\_core}, \protect\mdl{sbcblk\_clio})}}
+\section[Bulk formulation (\textit{sbcblk.F90})]
+{Bulk formulation (\protect\mdl{sbcblk})}
 \label{sec:SBC_blk}
-
-In the bulk formulation, the surface boundary condition fields are computed using bulk formulae and atmospheric fields and ocean (and ice) variables.
+%---------------------------------------namsbc_blk--------------------------------------------------
+
+\nlst{namsbc_blk}
+%--------------------------------------------------------------------------------------------------------------
+
+In the bulk formulation, the surface boundary condition fields are computed with bulk formulae using atmospheric fields 
+and ocean (and sea-ice) variables averaged over \np{nn\_fsbc} time-step.
 
 The atmospheric fields used depend on the bulk formulae used.
-Two bulk formulations are available:
-the CORE and the CLIO bulk formulea.
+In forced mode, when a sea-ice model is used, a specific bulk formulation is used.
+Therefore, different bulk formulae are used for the turbulent fluxes computation
+over the ocean and over sea-ice surface. 
+For the ocean, four bulk formulations are available thanks to the \href{https://brodeau.github.io/aerobulk/}{Aerobulk} package (\citet{brodeau.barnier.ea_JPO16}): 
+the NCAR (formerly named CORE), COARE 3.0, COARE 3.5 and ECMWF bulk formulae.
 The choice is made by setting to true one of the following namelist variable:
-\np{ln\_core} or \np{ln\_clio}.
-
-Note:
-in forced mode, when a sea-ice model is used, a bulk formulation (CLIO or CORE) have to be used.
-Therefore the two bulk (CLIO and CORE) formulea include the computation of the fluxes over
-both an ocean and an ice surface. 
-
-% -------------------------------------------------------------------------------------------------------------
-%        CORE Bulk formulea
-% -------------------------------------------------------------------------------------------------------------
-\subsection{CORE formulea (\protect\mdl{sbcblk\_core}, \protect\np{ln\_core}\forcode{ = .true.})}
-\label{subsec:SBC_blk_core}
-%------------------------------------------namsbc_core----------------------------------------------------
-%
-%\nlst{namsbc_core}
-%-------------------------------------------------------------------------------------------------------------
-
-The CORE bulk formulae have been developed by \citet{Large_Yeager_Rep04}.
-They have been designed to handle the CORE forcing, a mixture of NCEP reanalysis and satellite data.
-They use an inertial dissipative method to compute the turbulent transfer coefficients
-(momentum, sensible heat and evaporation) from the 10 metre wind speed, air temperature and specific humidity.
-This \citet{Large_Yeager_Rep04} dataset is available through
-the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
-
-Note that substituting ERA40 to NCEP reanalysis fields does not require changes in the bulk formulea themself.
-This is the so-called DRAKKAR Forcing Set (DFS) \citep{Brodeau_al_OM09}.
-
-Options are defined through the  \ngn{namsbc\_core} namelist variables.
-The required 8 input fields are:
+ \np{ln\_NCAR}, \np{ln\_COARE\_3p0},  \np{ln\_COARE\_3p5} and  \np{ln\_ECMWF}.
+For sea-ice, three possibilities can be selected:
+a constant transfer coefficient (1.4e-3; default value), \citet{lupkes.gryanik.ea_JGR12} (\np{ln\_Cd\_L12}), and \citet{lupkes.gryanik_JGR15} (\np{ln\_Cd\_L15}) parameterizations
+
+Common options are defined through the \ngn{namsbc\_blk} namelist variables.
+The required 9 input fields are:
 
 %--------------------------------------------------TABLE--------------------------------------------------
 \begin{table}[htbp]
-  \label{tab:CORE}
+  \label{tab:BULK}
   \begin{center}
     \begin{tabular}{|l|c|c|c|}
       \hline
-      Variable desciption              & Model variable  & Units   & point \\    \hline
-      i-component of the 10m air velocity & utau      & $m.s^{-1}$         & T  \\  \hline
-      j-component of the 10m air velocity & vtau      & $m.s^{-1}$         & T  \\  \hline
-      10m air temperature              & tair      & \r{}$K$            & T   \\ \hline
-      Specific humidity             & humi      & \%              & T \\      \hline
-      Incoming long wave radiation     & qlw    & $W.m^{-2}$         & T \\      \hline
-      Incoming short wave radiation    & qsr    & $W.m^{-2}$         & T \\      \hline
-      Total precipitation (liquid + solid)   & precip & $Kg.m^{-2}.s^{-1}$ & T \\   \hline
-      Solid precipitation              & snow      & $Kg.m^{-2}.s^{-1}$ & T \\   \hline
+      Variable description                           & Model variable   & Units                         & point \\   \hline
+      i-component of the 10m air velocity   & utau                   & $m.s^{-1}$                   & T         \\   \hline
+      j-component of the 10m air velocity   & vtau                & $m.s^{-1}$                   & T         \\   \hline
+      10m air temperature                      & tair                & \r{}$K$                        & T       \\   \hline
+      Specific humidity                        & humi           & \%                             & T      \\   \hline
+      Incoming long wave radiation          & qlw                & $W.m^{-2}$            & T        \\   \hline
+      Incoming short wave radiation          & qsr               & $W.m^{-2}$            & T        \\   \hline
+      Total precipitation (liquid + solid)         & precip            & $Kg.m^{-2}.s^{-1}$      & T      \\   \hline
+      Solid precipitation                           & snow               & $Kg.m^{-2}.s^{-1}$       & T      \\   \hline
+      Mean sea-level pressure                     & slp                     & $hPa$                          & T       \\ \hline
     \end{tabular}
   \end{center}
@@ -678 +682 @@
 \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
+Three multiplicative factors are available: 
+\np{rn\_pfac} and \np{rn\_efac} allow 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
-% -------------------------------------------------------------------------------------------------------------
-\subsection{CLIO formulea (\protect\mdl{sbcblk\_clio}, \protect\np{ln\_clio}\forcode{ = .true.})}
-\label{subsec:SBC_blk_clio}
-%------------------------------------------namsbc_clio----------------------------------------------------
-%
-%\nlst{namsbc_clio}
-%-------------------------------------------------------------------------------------------------------------
-
-The CLIO bulk formulae were developed several years ago for the Louvain-la-neuve coupled ice-ocean model
-(CLIO, \cite{Goosse_al_JGR99}). 
-They are simpler bulk formulae.
-They assume the stress to be known and compute the radiative fluxes from a climatological cloud cover. 
-
-Options are defined through the  \ngn{namsbc\_clio} namelist variables.
-The required 7 input fields are:
-
-%--------------------------------------------------TABLE--------------------------------------------------
-\begin{table}[htbp]
-  \label{tab:CLIO}
-  \begin{center}
-    \begin{tabular}{|l|l|l|l|}
-      \hline
-      Variable desciption           & Model variable  & Units           & point \\  \hline
-      i-component of the ocean stress     & utau         & $N.m^{-2}$         & U \\   \hline
-      j-component of the ocean stress     & vtau         & $N.m^{-2}$         & V \\   \hline
-      Wind speed module             & vatm         & $m.s^{-1}$         & T \\   \hline
-      10m air temperature              & tair         & \r{}$K$            & T \\   \hline
-      Specific humidity                & humi         & \%              & T \\   \hline
-      Cloud cover                   &           & \%              & T \\   \hline
-      Total precipitation (liquid + solid)   & precip    & $Kg.m^{-2}.s^{-1}$ & T \\   \hline
-      Solid precipitation              & snow         & $Kg.m^{-2}.s^{-1}$ & T \\   \hline
-    \end{tabular}
-  \end{center}
-\end{table}
-%--------------------------------------------------------------------------------------------------------------
+Its range must be between zero and one, and it is recommended to set it to 0 at low-resolution (ORCA2 configuration).
 
 As for the flux formulation, information about the input data required by the model is provided in
-the namsbc\_blk\_core or namsbc\_blk\_clio namelist (see \autoref{subsec:SBC_fldread}). 
+the namsbc\_blk namelist (see \autoref{subsec:SBC_fldread}). 
+
+
+% -------------------------------------------------------------------------------------------------------------
+%        Ocean-Atmosphere Bulk formulae
+% -------------------------------------------------------------------------------------------------------------
+\subsection{Ocean-Atmosphere Bulk formulae}
+%\subsection[Ocean-Atmosphere Bulk formulae (\textit{sbcblk_algo\{\_ncar,\_coare,\_coare3p5,\_ecmwf}.F90})]
+\label{subsec:SBC_blk_ocean}
+
+Four different bulk algorithms are available to compute surface turbulent momentum and heat fluxes over the ocean.
+COARE 3.0, COARE 3.5 and ECMWF schemes mainly differ by their roughness lenghts computation and consequently 
+their neutral transfer coefficients relationships with neutral wind.
+\begin{itemize}
+\item
+  NCAR (\np{ln\_NCAR}\forcode{ = .true.}):
+  The NCAR bulk formulae have been developed by \citet{large.yeager_rpt04}.
+  They have been designed to handle the NCAR forcing, a mixture of NCEP reanalysis and satellite data.
+  They use an inertial dissipative method to compute the turbulent transfer coefficients
+  (momentum, sensible heat and evaporation) from the 10m wind speed, air temperature and specific humidity.
+  This \citet{large.yeager_rpt04} dataset is available through
+  the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/NCAR.html}{GFDL web site}.
+  Note that substituting ERA40 to NCEP reanalysis fields does not require changes in the bulk formulea themself.
+  This is the so-called DRAKKAR Forcing Set (DFS) \citep{brodeau.barnier.ea_OM10}.
+\item
+  COARE 3.0 (\np{ln\_COARE\_3p0}\forcode{ = .true.}): 
+  See \citet{fairall.bradley.ea_JC03} for more details
+\item
+  COARE 3.5 (\np{ln\_COARE\_3p5}\forcode{ = .true.}): 
+  See \citet{edson.jampana.ea_JPO13} for more details
+\item
+  ECMWF (\np{ln\_ECMWF}\forcode{ = .true.}): 
+  Based on \href{https://www.ecmwf.int/node/9221}{IFS (Cy31)} implementation and documentation.
+  Surface roughness lengths needed for the Obukhov length are computed following \citet{beljaars_QJRMS95}.
+\end{itemize}
+
+
+% -------------------------------------------------------------------------------------------------------------
+%        Ice-Atmosphere Bulk formulae
+% -------------------------------------------------------------------------------------------------------------
+\subsection{ Ice-Atmosphere Bulk formulae }
+\label{subsec:SBC_blk_ice}
+
+Surface turbulent fluxes between sea-ice and the atmosphere can be computed in three different ways:
+
+\begin{itemize}
+\item
+  Constant value (\np{constant\ value}\forcode{ Cd_ice = 1.4e-3 }):
+  default constant value used for momentum and heat neutral transfer coefficients
+\item
+  \citet{lupkes.gryanik.ea_JGR12} (\np{ln\_Cd\_L12}\forcode{ = .true.}):
+  This scheme adds a dependency on edges at leads, melt ponds and flows
+  of the constant neutral air-ice drag. After some approximations, 
+  this can be resumed to a dependency on ice concentration (A).
+  This drag coefficient has a parabolic shape (as a function of ice concentration)
+  starting at 1.5e-3 for A=0, reaching 1.97e-3 for A=0.5 and going down 1.4e-3 for A=1.
+  It is theoretically applicable to all ice conditions (not only MIZ).
+\item
+  \citet{lupkes.gryanik_JGR15} (\np{ln\_Cd\_L15}\forcode{ = .true.}):
+  Alternative turbulent transfer coefficients formulation between sea-ice 
+  and atmosphere with distinct momentum and heat coefficients depending 
+  on sea-ice concentration and atmospheric stability (no melt-ponds effect for now).
+  The parameterization is adapted from ECHAM6 atmospheric model.
+  Compared to Lupkes2012 scheme, it considers specific skin and form drags
+  to compute neutral transfer coefficients for both heat and momentum fluxes.
+  Atmospheric stability effect on transfer coefficient is also taken into account.
+\end{itemize}
+
+
 
 % ================================================================
 % Coupled formulation
 % ================================================================
-\section{Coupled formulation (\protect\mdl{sbccpl})}
+\section[Coupled formulation (\textit{sbccpl.F90})]
+{Coupled formulation (\protect\mdl{sbccpl})}
 \label{sec:SBC_cpl}
 %------------------------------------------namsbc_cpl----------------------------------------------------
@@ -737 +772 @@
 
 In the coupled formulation of the surface boundary condition,
-the fluxes are provided by the OASIS coupler at a frequency which is defined in the OASIS coupler,
+the fluxes are provided by the OASIS coupler at a frequency which is defined in the OASIS coupler namelist,
 while sea and ice surface temperature, ocean and ice albedo, and ocean currents are sent to
 the atmospheric component.
 
 A generalised coupled interface has been developed.
-It is currently interfaced with OASIS-3-MCT (\key{oasis3}).
+It is currently interfaced with OASIS-3-MCT versions 1 to 4 (\key{oasis3}).
+An additional specific CPP key (\key{oa3mct\_v1v2}) is needed for OASIS-3-MCT versions 1 and 2.
 It has been successfully used to interface \NEMO to most of the European atmospheric GCM
 (ARPEGE, ECHAM, ECMWF, HadAM, HadGAM, LMDz), as well as to \href{http://wrf-model.org/}{WRF}
 (Weather Research and Forecasting Model).
 
-Note that in addition to the setting of \np{ln\_cpl} to true, the \key{coupled} have to be defined.
-The CPP key is mainly used in sea-ice to ensure that the atmospheric fluxes are actually received by
-the ice-ocean system (no calculation of ice sublimation in coupled mode).
-When PISCES biogeochemical model (\key{top} and \key{pisces}) is also used in the coupled system, 
-the whole carbon cycle is computed by defining \key{cpl\_carbon\_cycle}.
+When PISCES biogeochemical model (\key{top}) is also used in the coupled system, 
+the whole carbon cycle is computed.
 In this case, CO$_2$ fluxes will be exchanged between the atmosphere and the ice-ocean system
 (and need to be activated in \ngn{namsbc{\_}cpl} ).
@@ -757 +790 @@
 The namelist above allows control of various aspects of the coupling fields (particularly for vectors) and
 now allows for any coupling fields to have multiple sea ice categories (as required by LIM3 and CICE).
-When indicating a multi-category coupling field in namsbc{\_}cpl the number of categories will be determined by
+When indicating a multi-category coupling field in \ngn{namsbc{\_}cpl}, the number of categories will be determined by
 the number used in the sea ice model.
-In some limited cases it may be possible to specify single category coupling fields even when
+In some limited cases, it may be possible to specify single category coupling fields even when
 the sea ice model is running with multiple categories -
-in this case the user should examine the code to be sure the assumptions made are satisfactory.
-In cases where this is definitely not possible the model should abort with an error message.
-The new code has been tested using ECHAM with LIM2, and HadGAM3 with CICE but
-although it will compile with \key{lim3} additional minor code changes may be required to run using LIM3.
+in this case, the user should examine the code to be sure the assumptions made are satisfactory.
+In cases where this is definitely not possible, the model should abort with an error message.
+
 
 
@@ -770 +802 @@
 %        Atmospheric pressure
 % ================================================================
-\section{Atmospheric pressure (\protect\mdl{sbcapr})}
+\section[Atmospheric pressure (\textit{sbcapr.F90})]
+{Atmospheric pressure (\protect\mdl{sbcapr})}
 \label{sec:SBC_apr}
 %------------------------------------------namsbc_apr----------------------------------------------------
@@ -778 +811 @@
 
 The optional atmospheric pressure can be used to force ocean and ice dynamics
-(\np{ln\_apr\_dyn}\forcode{ = .true.}, \textit{\ngn{namsbc}} namelist).
-The input atmospheric forcing defined via \np{sn\_apr} structure (\textit{namsbc\_apr} namelist)
+(\np{ln\_apr\_dyn}\forcode{ = .true.}, \ngn{namsbc} namelist).
+The input atmospheric forcing defined via \np{sn\_apr} structure (\ngn{namsbc\_apr} namelist)
 can be interpolated in time to the model time step, and even in space when the interpolation on-the-fly is used.
 When used to force the dynamics, the atmospheric pressure is further transformed into
@@ -789 +822 @@
 where $P_{atm}$ is the atmospheric pressure and $P_o$ a reference atmospheric pressure.
 A value of $101,000~N/m^2$ is used unless \np{ln\_ref\_apr} is set to true.
-In this case $P_o$ is set to the value of $P_{atm}$ averaged over the ocean domain,
-\ie the mean value of $\eta_{ib}$ is kept to zero at all time step.
+In this case, $P_o$ is set to the value of $P_{atm}$ averaged over the ocean domain,
+\ie the mean value of $\eta_{ib}$ is kept to zero at all time steps.
 
 The gradient of $\eta_{ib}$ is added to the RHS of the ocean momentum equation (see \mdl{dynspg} for the ocean).
 For sea-ice, the sea surface height, $\eta_m$, which is provided to the sea ice model is set to $\eta - \eta_{ib}$
 (see \mdl{sbcssr} module).
-$\eta_{ib}$ can be set in the output.
+$\eta_{ib}$ can be written in the output.
 This can simplify altimetry data and model comparison as
 inverse barometer sea surface height is usually removed from these date prior to their distribution.
@@ -803 +836 @@
 \np{ln\_apr\_obc}  might be set to true.
 
+
+
 % ================================================================
 %        Surface Tides Forcing
 % ================================================================
-\section{Surface tides (\protect\mdl{sbctide})}
+\section[Surface tides (\textit{sbctide.F90})]
+{Surface tides (\protect\mdl{sbctide})}
 \label{sec:SBC_tide}
 
@@ -819 +855 @@
 \[
   % \label{eq:PE_dyn_tides}
-  \frac{\partial {\rm {\bf U}}_h }{\partial t}= ...
+  \frac{\partial {\mathrm {\mathbf U}}_h }{\partial t}= ...
   +g\nabla (\Pi_{eq} + \Pi_{sal})
 \]
@@ -827 +863 @@
 The equilibrium tidal forcing is expressed as a sum over a subset of
 constituents chosen from the set of available tidal constituents
-defined in file \rou{SBC/tide.h90} (this comprises the tidal
+defined in file \textit{SBC/tide.h90} (this comprises the tidal
 constituents \textit{M2, N2, 2N2, S2, K2, K1, O1, Q1, P1, M4, Mf, Mm,
   Msqm, Mtm, S1, MU2, NU2, L2}, and \textit{T2}). Individual
@@ -839 +875 @@
 
 The SAL term should in principle be computed online as it depends on
-the model tidal prediction itself (see \citet{Arbic2004} for a
+the model tidal prediction itself (see \citet{arbic.garner.ea_DSR04} for a
 discussion about the practical implementation of this term).
 Nevertheless, the complex calculations involved would make this
-computationally too expensive.  Here, two options are available:
+computationally too expensive. Here, two options are available:
 $\Pi_{sal}$ generated by an external model can be read in
 (\np{ln\_read\_load=.true.}), or a ``scalar approximation'' can be
@@ -854 +890 @@
 \forcode{.false.} removes the SAL contribution.
 
+
+
 % ================================================================
 %        River runoffs
 % ================================================================
-\section{River runoffs (\protect\mdl{sbcrnf})}
+\section[River runoffs (\textit{sbcrnf.F90})]
+{River runoffs (\protect\mdl{sbcrnf})}
 \label{sec:SBC_rnf}
 %------------------------------------------namsbc_rnf----------------------------------------------------
@@ -871 +910 @@
 %coastal modelling and becomes more and more often open ocean and climate modelling 
 %\footnote{At least a top cells thickness of 1~meter and a 3 hours forcing frequency are
-%required to properly represent the diurnal cycle \citep{Bernie_al_JC05}. see also \autoref{fig:SBC_dcy}.}.
+%required to properly represent the diurnal cycle \citep{bernie.woolnough.ea_JC05}. see also \autoref{fig:SBC_dcy}.}.
 
 
@@ -892 +931 @@
 \footnote{
   At least a top cells thickness of 1~meter and a 3 hours forcing frequency are required to
-  properly represent the diurnal cycle \citep{Bernie_al_JC05}.
+  properly represent the diurnal cycle \citep{bernie.woolnough.ea_JC05}.
   see also \autoref{fig:SBC_dcy}.}.
 
@@ -935 +974 @@
 As such the volume of water does not change, but the water is diluted.
 
-For the non-linear free surface case (\key{vvl}), no flux is allowed through the surface.
+For the non-linear free surface case, no flux is allowed through the surface.
 Instead in the surface box (as well as water moving up from the boxes below) a volume of runoff water is added with
 no corresponding heat and salt addition and so as happens in the lower boxes there is a dilution effect.
@@ -978 +1017 @@
 %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:
 
-%}
+
+
 % ================================================================
 %        Ice shelf melting
 % ================================================================
-\section{Ice shelf melting (\protect\mdl{sbcisf})}
+\section[Ice shelf melting (\textit{sbcisf.F90})]
+{Ice shelf melting (\protect\mdl{sbcisf})}
 \label{sec:SBC_isf}
 %------------------------------------------namsbc_isf----------------------------------------------------
@@ -988 +1029 @@
 \nlst{namsbc_isf}
 %--------------------------------------------------------------------------------------------------------
+
 The namelist variable in \ngn{namsbc}, \np{nn\_isf}, controls the ice shelf representation.
-Description and result of sensitivity test to \np{nn\_isf} are presented in \citet{Mathiot2017}. 
+Description and result of sensitivity test to \np{nn\_isf} are presented in \citet{mathiot.jenkins.ea_GMD17}. 
 The different options are illustrated in \autoref{fig:SBC_isf}.
 
 \begin{description}
-\item[\np{nn\_isf}\forcode{ = 1}]:
+
+  \item[\np{nn\_isf}\forcode{ = 1}]:
   The ice shelf cavity is represented (\np{ln\_isfcav}\forcode{ = .true.} needed).
   The fwf and heat flux are depending of the local water properties.
+  
   Two different bulk formulae are available:
 
@@ -1001 +1045 @@
    \item[\np{nn\_isfblk}\forcode{ = 1}]:
      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{Hunter2006}.
+     the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}.
    \item[\np{nn\_isfblk}\forcode{ = 2}]:
      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{Jenkins1991}.
+     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{Losch2008}. 
+     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}.
      The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the the first \np{rn\_hisf\_tbl} m.
@@ -1038 +1082 @@
 \]
      where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn\_hisf\_tbl} meters).
-     See \citet{Jenkins2010} for all the details on this formulation. It is the recommended formulation for realistic application.
+     See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application.
    \item[\np{nn\_gammablk}\forcode{ = 2}]:
      The salt and heat exchange coefficients are velocity and stability dependent and defined as:
@@ -1047 +1091 @@
      $\Gamma_{Turb}$ the contribution of the ocean stability and
      $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion.
-     See \citet{Holland1999} for all the details on this formulation. 
+     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{nn\_isf}\forcode{ = 2}]:
+  \item[\np{nn\_isf}\forcode{ = 2}]:
    The ice shelf cavity is not represented.
-   The fwf and heat flux are computed using the \citet{Beckmann2003} parameterisation of isf melting.
+   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}) and the base of the ice shelf along the calving front
    (\np{sn\_depmin\_isf}) as in (\np{nn\_isf}\forcode{ = 3}).
    The effective melting length (\np{sn\_Leff\_isf}) is read from a file.
- \item[\np{nn\_isf}\forcode{ = 3}]:
+  \item[\np{nn\_isf}\forcode{ = 3}]:
    The ice shelf cavity is not represented.
    The fwf (\np{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between
@@ -1063 +1107 @@
    the base of the ice shelf along the calving front (\np{sn\_depmin\_isf}).
    The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.
- \item[\np{nn\_isf}\forcode{ = 4}]:
+  \item[\np{nn\_isf}\forcode{ = 4}]:
    The ice shelf cavity is opened (\np{ln\_isfcav}\forcode{ = .true.} needed).
    However, the fwf is not computed but specified from file \np{sn\_fwfisf}).
@@ -1089 +1133 @@
 \begin{figure}[!t]
   \begin{center}
-    \includegraphics[width=0.8\textwidth]{Fig_SBC_isf}
+    \includegraphics[width=\textwidth]{Fig_SBC_isf}
     \caption{
       \protect\label{fig:SBC_isf}
@@ -1098 +1142 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
+
+
+% ================================================================
+%        Ice sheet coupling
+% ================================================================
 \section{Ice sheet coupling}
 \label{sec:SBC_iscpl}
@@ -1104 +1153 @@
 \nlst{namsbc_iscpl}
 %--------------------------------------------------------------------------------------------------------
+
 Ice sheet/ocean coupling is done through file exchange at the restart step.
 At each restart step:
+
 \begin{description}
 \item[Step 1]: the ice sheet model send a new bathymetry and ice shelf draft netcdf file.
@@ -1117 +1168 @@
 potentially some new wet/dry cells due to the ice sheet dynamics/thermodynamics.
 The wetting and drying scheme applied on the restart is very simple and described below for the 6 different possible cases:
+
 \begin{description}
 \item[Thin a cell down]:
@@ -1155 +1207 @@
 The corrective increment is apply into the cell itself (if it is a wet cell), the neigbouring cells or the closest wet cell (if the cell is now dry).
 
-%
+
+
 % ================================================================
 %        Handling of icebergs
@@ -1166 +1219 @@
 %-------------------------------------------------------------------------------------------------------------
 
-Icebergs are modelled as lagrangian particles in NEMO \citep{Marsh_GMD2015}.
-Their physical behaviour is controlled by equations as described in \citet{Martin_Adcroft_OM10} ).
+Icebergs are modelled as lagrangian particles in NEMO \citep{marsh.ivchenko.ea_GMD15}.
+Their physical behaviour is controlled by equations as described in \citet{martin.adcroft_OM10} ).
 (Note that the authors kindly provided a copy of their code to act as a basis for implementation in NEMO).
 Icebergs are initially spawned into one of ten classes which have specific mass and thickness as
@@ -1186 +1239 @@
   the geographical box: lonmin,lonmax,latmin,latmax
 \item[\np{nn\_test\_icebergs}\forcode{ = -1}]
-  In this scheme the model reads a calving file supplied in the \np{sn\_icb} parameter.
+  In this scheme, the model reads a calving file supplied in the \np{sn\_icb} parameter.
   This should be a file with a field on the configuration grid (typically ORCA)
   representing ice accumulation rate at each model point.
@@ -1224 +1277 @@
 since its trajectory data may be spread across multiple files.
 
-% -------------------------------------------------------------------------------------------------------------
+
+
+% =============================================================================================================
 %        Interactions with waves (sbcwave.F90, ln_wave)
-% -------------------------------------------------------------------------------------------------------------
-\section{Interactions with waves (\protect\mdl{sbcwave}, \protect\np{ln\_wave})}
+% =============================================================================================================
+\section[Interactions with waves (\textit{sbcwave.F90}, \texttt{ln\_wave})]
+{Interactions with waves (\protect\mdl{sbcwave}, \protect\np{ln\_wave})}
 \label{sec:SBC_wave}
 %------------------------------------------namsbc_wave--------------------------------------------------------
@@ -1241 +1297 @@
 
 Physical processes related to ocean surface waves can be accounted by setting the logical variable 
-\np{ln\_wave}\forcode{= .true.} in \ngn{namsbc} namelist. In addition, specific flags accounting for 
-different porcesses should be activated as explained in the following sections.
+\np{ln\_wave} \forcode{= .true.} in \ngn{namsbc} namelist. In addition, specific flags accounting for 
+different processes should be activated as explained in the following sections.
 
 Wave fields can be provided either in forced or coupled mode:
@@ -1254 +1310 @@
 
 
-% ================================================================
+% ----------------------------------------------------------------
 % Neutral drag coefficient from wave model (ln_cdgw)
 
-% ================================================================
-\subsection{Neutral drag coefficient from wave model (\protect\np{ln\_cdgw})}
+% ----------------------------------------------------------------
+\subsection[Neutral drag coefficient from wave model (\texttt{ln\_cdgw})]
+{Neutral drag coefficient from wave model (\protect\np{ln\_cdgw})}
 \label{subsec:SBC_wave_cdgw}
 
 The neutral surface drag coefficient provided from an external data source (\ie a wave model), 
 can be used by setting the logical variable \np{ln\_cdgw} \forcode{= .true.} in \ngn{namsbc} namelist. 
-Then using the routine \rou{turb\_ncar} and starting from the neutral drag coefficent provided, 
+Then using the routine \rou{sbcblk\_algo\_ncar} and starting from the neutral drag coefficent provided, 
 the drag coefficient is computed according to the stable/unstable conditions of the 
-air-sea interface following \citet{Large_Yeager_Rep04}. 
-
-
-% ================================================================
+air-sea interface following \citet{large.yeager_rpt04}. 
+
+
+% ----------------------------------------------------------------
 % 3D Stokes Drift (ln_sdw, nn_sdrift)
-% ================================================================
-\subsection{3D Stokes Drift (\protect\np{ln\_sdw, nn\_sdrift})}
+% ----------------------------------------------------------------
+\subsection[3D Stokes Drift (\texttt{ln\_sdw}, \texttt{nn\_sdrift})]
+{3D Stokes Drift (\protect\np{ln\_sdw, nn\_sdrift})}
 \label{subsec:SBC_wave_sdw}
 
-The Stokes drift is a wave driven mechanism of mass and momentum transport \citep{Stokes_1847}. 
+The Stokes drift is a wave driven mechanism of mass and momentum transport \citep{stokes_ibk09}. 
 It is defined as the difference between the average velocity of a fluid parcel (Lagrangian velocity) 
 and the current measured at a fixed point (Eulerian velocity). 
 As waves travel, the water particles that make up the waves travel in orbital motions but 
 without a closed path. Their movement is enhanced at the top of the orbit and slowed slightly 
-at the bottom so the result is a net forward motion of water particles, referred to as the Stokes drift. 
+at the bottom, so the result is a net forward motion of water particles, referred to as the Stokes drift. 
 An accurate evaluation of the Stokes drift and the inclusion of related processes may lead to improved 
-representation of surface physics in ocean general circulation models.
+representation of surface physics in ocean general circulation models. %GS: reference needed
 The Stokes drift velocity $\mathbf{U}_{st}$ in deep water can be computed from the wave spectrum and may be written as: 
 
@@ -1296 +1354 @@
 $k=\frac{2\pi}{\lambda}$ (being $\lambda$ the wavelength). \\
 
-In order to evaluate the Stokes drift in a realistic ocean wave field the wave spectral shape is required 
+In order to evaluate the Stokes drift in a realistic ocean wave field, the wave spectral shape is required 
 and its computation quickly becomes expensive as the 2D spectrum must be integrated for each vertical level. 
 To simplify, it is customary to use approximations to the full Stokes profile.
@@ -1307 +1365 @@
 \begin{description}
 \item[\np{nn\_sdrift} = 0]: exponential integral profile parameterization proposed by 
-\citet{Breivik_al_JPO2014}:
+\citet{breivik.janssen.ea_JPO14}:
 
 \[
@@ -1326 +1384 @@
 
 \item[\np{nn\_sdrift} = 1]: velocity profile based on the Phillips spectrum which is considered to be a 
-reasonable estimate of the part of the spectrum most contributing to the Stokes drift velocity near the surface
-\citep{Breivik_al_OM2016}:
+reasonable estimate of the part of the spectrum mostly contributing to the Stokes drift velocity near the surface
+\citep{breivik.bidlot.ea_OM16}:
 
 \[
@@ -1364 +1422 @@
 
 
-% ================================================================
+% ----------------------------------------------------------------
 % Stokes-Coriolis term (ln_stcor)
-% ================================================================
-\subsection{Stokes-Coriolis term (\protect\np{ln\_stcor})}
+% ----------------------------------------------------------------
+\subsection[Stokes-Coriolis term (\texttt{ln\_stcor})]
+{Stokes-Coriolis term (\protect\np{ln\_stcor})}
 \label{subsec:SBC_wave_stcor}
 
@@ -1378 +1437 @@
 
 
-% ================================================================
+% ----------------------------------------------------------------
 % Waves modified stress (ln_tauwoc, ln_tauw)
-% ================================================================
-\subsection{Wave modified sress (\protect\np{ln\_tauwoc, ln\_tauw})} 
+% ----------------------------------------------------------------
+\subsection[Wave modified stress (\texttt{ln\_tauwoc}, \texttt{ln\_tauw})]
+{Wave modified sress (\protect\np{ln\_tauwoc, ln\_tauw})}
 \label{subsec:SBC_wave_tauw}
 
 The surface stress felt by the ocean is the atmospheric stress minus the net stress going 
-into the waves \citep{Janssen_al_TM13}. Therefore, when waves are growing, momentum and energy is spent and is not 
+into the waves \citep{janssen.breivik.ea_rpt13}. Therefore, when waves are growing, momentum and energy is spent and is not 
 available for forcing the mean circulation, while in the opposite case of a decaying sea 
-state more momentum is available for forcing the ocean. 
-Only when the sea state is in equilibrium the ocean is forced by the atmospheric stress, 
-but in practice an equilibrium sea state is a fairly rare event. 
+state, more momentum is available for forcing the ocean. 
+Only when the sea state is in equilibrium, the ocean is forced by the atmospheric stress, 
+but in practice, an equilibrium sea state is a fairly rare event. 
 So the atmospheric stress felt by the ocean circulation $\tau_{oc,a}$ can be expressed as: 
 
@@ -1419 +1479 @@
 
 
+
 % ================================================================
 % Miscellanea options
@@ -1425 +1486 @@
 \label{sec:SBC_misc}
 
+
 % -------------------------------------------------------------------------------------------------------------
 %        Diurnal cycle
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Diurnal cycle (\protect\mdl{sbcdcy})}
+\subsection[Diurnal cycle (\textit{sbcdcy.F90})]
+{Diurnal cycle (\protect\mdl{sbcdcy})}
 \label{subsec:SBC_dcy}
-%------------------------------------------namsbc_rnf----------------------------------------------------
+%------------------------------------------namsbc-------------------------------------------------------------
 %
 \nlst{namsbc} 
@@ -1438 +1501 @@
 \begin{figure}[!t]
   \begin{center}
-    \includegraphics[width=0.8\textwidth]{Fig_SBC_diurnal}
+    \includegraphics[width=\textwidth]{Fig_SBC_diurnal}
     \caption{
       \protect\label{fig:SBC_diurnal}
@@ -1445 +1508 @@
       the mean value of the analytical cycle (blue line) over a time step,
       not as the mid time step value of the analytically cycle (red square).
-      From \citet{Bernie_al_CD07}.
+      From \citet{bernie.guilyardi.ea_CD07}.
     }
   \end{center}
@@ -1451 +1514 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
-\cite{Bernie_al_JC05} have shown that to capture 90$\%$ of the diurnal variability of SST requires a vertical resolution in upper ocean of 1~m or better and a temporal resolution of the surface fluxes of 3~h or less.
-Unfortunately high frequency forcing fields are rare, not to say inexistent.
-Nevertheless, it is possible to obtain a reasonable diurnal cycle of the SST knowning only short wave flux (SWF) at
-high frequency \citep{Bernie_al_CD07}.
+\cite{bernie.woolnough.ea_JC05} have shown that to capture 90$\%$ of the diurnal variability of SST requires a vertical resolution in upper ocean of 1~m or better and a temporal resolution of the surface fluxes of 3~h or less.
+%Unfortunately high frequency forcing fields are rare, not to say inexistent. GS: not true anymore !
+Nevertheless, it is possible to obtain a reasonable diurnal cycle of the SST knowning only short wave flux (SWF) at high frequency \citep{bernie.guilyardi.ea_CD07}.
 Furthermore, only the knowledge of daily mean value of SWF is needed,
 as higher frequency variations can be reconstructed from them,
 assuming that the diurnal cycle of SWF is a scaling of the top of the atmosphere diurnal cycle of incident SWF.
-The \cite{Bernie_al_CD07} reconstruction algorithm is available in \NEMO by
+The \cite{bernie.guilyardi.ea_CD07} reconstruction algorithm is available in \NEMO by
 setting \np{ln\_dm2dc}\forcode{ = .true.} (a \textit{\ngn{namsbc}} namelist variable) when
-using CORE bulk formulea (\np{ln\_blk\_core}\forcode{ = .true.}) or
+using a bulk formulation (\np{ln\_blk}\forcode{ = .true.}) or
 the flux formulation (\np{ln\_flx}\forcode{ = .true.}).
 The reconstruction is performed in the \mdl{sbcdcy} module.
-The detail of the algoritm used can be found in the appendix~A of \cite{Bernie_al_CD07}.
-The algorithm preserve the daily mean incoming SWF as the reconstructed SWF at
+The detail of the algoritm used can be found in the appendix~A of \cite{bernie.guilyardi.ea_CD07}.
+The algorithm preserves the daily mean incoming SWF as the reconstructed SWF at
 a given time step is the mean value of the analytical cycle over this time step (\autoref{fig:SBC_diurnal}).
 The use of diurnal cycle reconstruction requires the input SWF to be daily
-(\ie a frequency of 24 and a time interpolation set to true in \np{sn\_qsr} namelist parameter).
-Furthermore, it is recommended to have a least 8 surface module time step per day,
+(\ie a frequency of 24 hours and a time interpolation set to true in \np{sn\_qsr} namelist parameter).
+Furthermore, it is recommended to have a least 8 surface module time steps per day,
 that is  $\rdt \ nn\_fsbc < 10,800~s = 3~h$.
 An example of recontructed SWF is given in \autoref{fig:SBC_dcy} for a 12 reconstructed diurnal cycle,
@@ -1476 +1538 @@
 \begin{figure}[!t]
   \begin{center}
-    \includegraphics[width=0.7\textwidth]{Fig_SBC_dcy}
+    \includegraphics[width=\textwidth]{Fig_SBC_dcy}
     \caption{
       \protect\label{fig:SBC_dcy}
@@ -1491 +1553 @@
 an inconsistency between the scale of the vertical resolution and the forcing acting on that scale.
 
+
 % -------------------------------------------------------------------------------------------------------------
 %        Rotation of vector pairs onto the model grid directions
@@ -1497 +1560 @@
 \label{subsec:SBC_rotation}
 
-When using a flux (\np{ln\_flx}\forcode{ = .true.}) or
-bulk (\np{ln\_clio}\forcode{ = .true.} or \np{ln\_core}\forcode{ = .true.}) formulation,
+When using a flux (\np{ln\_flx}\forcode{ = .true.}) or bulk (\np{ln\_blk}\forcode{ = .true.}) formulation,
 pairs of vector components can be rotated from east-north directions onto the local grid directions.
 This is particularly useful when interpolation on the fly is used since here any vectors are likely to
 be defined relative to a rectilinear grid.
-To activate this option a non-empty string is supplied in the rotation pair column of the relevant namelist.
+To activate this option, a non-empty string is supplied in the rotation pair column of the relevant namelist.
 The eastward component must start with "U" and the northward component with "V".  
 The remaining characters in the strings are used to identify which pair of components go together.
@@ -1511 +1573 @@
 The rot\_rep routine from the \mdl{geo2ocean} module is used to perform the rotation.
 
+
 % -------------------------------------------------------------------------------------------------------------
 %        Surface restoring to observed SST and/or SSS
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Surface restoring to observed SST and/or SSS (\protect\mdl{sbcssr})}
+\subsection[Surface restoring to observed SST and/or SSS (\textit{sbcssr.F90})]
+{Surface restoring to observed SST and/or SSS (\protect\mdl{sbcssr})}
 \label{subsec:SBC_ssr}
 %------------------------------------------namsbc_ssr----------------------------------------------------
@@ -1521 +1585 @@
 %-------------------------------------------------------------------------------------------------------------
 
-IOptions are defined through the \ngn{namsbc\_ssr} namelist variables.
+Options are defined through the \ngn{namsbc\_ssr} namelist variables.
 On forced mode using a flux formulation (\np{ln\_flx}\forcode{ = .true.}),
 a feedback term \emph{must} be added to the surface heat flux $Q_{ns}^o$:
@@ -1546 +1610 @@
 (observed, climatological or an atmospheric model product),
 \textit{SSS}$_{Obs}$ is a sea surface salinity
-(usually a time interpolation of the monthly mean Polar Hydrographic Climatology \citep{Steele2001}),
+(usually a time interpolation of the monthly mean Polar Hydrographic Climatology \citep{steele.morley.ea_JC01}),
 $\left.S\right|_{k=1}$ is the model surface layer salinity and
 $\gamma_s$ is a negative feedback coefficient which is provided as a namelist parameter.
 Unlike heat flux, there is no physical justification for the feedback term in \autoref{eq:sbc_dmp_emp} as
-the atmosphere does not care about ocean surface salinity \citep{Madec1997}.
+the atmosphere does not care about ocean surface salinity \citep{madec.delecluse_IWN97}.
 The SSS restoring term should be viewed as a flux correction on freshwater fluxes to
 reduce the uncertainties we have on the observed freshwater budget.
+
 
 % -------------------------------------------------------------------------------------------------------------
@@ -1578 +1643 @@
   This prevents deep convection to occur when trying to reach the freezing point
   (and so ice covered area condition) while the SSS is too large.
-  This manner of managing sea-ice area, just by using si IF case,
+  This manner of managing sea-ice area, just by using a IF case,
   is usually referred as the \textit{ice-if} model.
   It can be found in the \mdl{sbcice{\_}if} module.
@@ -1585 +1650 @@
   This model computes the ice-ocean fluxes,
   that are combined with the air-sea fluxes using the ice fraction of each model cell to
-  provide the surface ocean fluxes.
-  Note that the activation of a sea-ice model is is done by defining a CPP key (\key{lim3} or \key{cice}).
+  provide the surface averaged ocean fluxes.
+  Note that the activation of a sea-ice model is done by defining a CPP key (\key{si3} or \key{cice}).
   The activation automatically overwrites the read value of nn{\_}ice to its appropriate value
-  (\ie $2$ for LIM-3 or $3$ for CICE).
+  (\ie $2$ for SI3 or $3$ for CICE).
 \end{description}
 
 % {Description of Ice-ocean interface to be added here or in LIM 2 and 3 doc ?}
-
-\subsection{Interface to CICE (\protect\mdl{sbcice\_cice})}
+%GS: ocean-ice (SI3) interface is not located in SBC directory anymore, so it should be included in SI3 doc
+
+
+% -------------------------------------------------------------------------------------------------------------
+%        CICE-ocean Interface
+% -------------------------------------------------------------------------------------------------------------
+\subsection[Interface to CICE (\textit{sbcice\_cice.F90})]
+{Interface to CICE (\protect\mdl{sbcice\_cice})}
 \label{subsec:SBC_cice}
 
-It is now possible to couple a regional or global NEMO configuration (without AGRIF)
+It is possible to couple a regional or global NEMO configuration (without AGRIF)
 to the CICE sea-ice model by using \key{cice}.
 The CICE code can be obtained from \href{http://oceans11.lanl.gov/trac/CICE/}{LANL} and
@@ -1603 +1674 @@
 and CICE CPP keys \textbf{ORCA\_GRID}, \textbf{CICE\_IN\_NEMO} and \textbf{coupled} should be used
 (seek advice from UKMO if necessary).
-Currently the code is only designed to work when using the CORE forcing option for NEMO
+Currently, the code is only designed to work when using the NCAR forcing option for NEMO %GS: still true ?
 (with \textit{calc\_strair}\forcode{ = .true.} and \textit{calc\_Tsfc}\forcode{ = .true.} in the CICE name-list),
 or alternatively when NEMO is coupled to the HadGAM3 atmosphere model
@@ -1623 +1694 @@
 there is no sea ice.
 
+
 % -------------------------------------------------------------------------------------------------------------
 %        Freshwater budget control 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Freshwater budget control (\protect\mdl{sbcfwb})}
+\subsection[Freshwater budget control (\textit{sbcfwb.F90})]
+{Freshwater budget control (\protect\mdl{sbcfwb})}
 \label{subsec:SBC_fwb}
 
-For global ocean simulation it can be useful to introduce a control of the mean sea level in order to
+For global ocean simulation, it can be useful to introduce a control of the mean sea level in order to
 prevent unrealistic drift of the sea surface height due to inaccuracy in the freshwater fluxes.
-In \NEMO, two way of controlling the the freshwater budget. 
+In \NEMO, two way of controlling the freshwater budget are proposed:
+ 
 \begin{description}
 \item[\np{nn\_fwb}\forcode{ = 0}]
@@ -1638 +1712 @@
 \item[\np{nn\_fwb}\forcode{ = 1}]
   global mean \textit{emp} set to zero at each model time step. 
-%Note that with a sea-ice model, this technique only control the mean sea level with linear free surface (\key{vvl} not defined) and no mass flux between ocean and ice (as it is implemented in the current ice-ocean coupling). 
+  %GS: comment below still relevant ?
+  %Note that with a sea-ice model, this technique only controls the mean sea level with linear free surface and no mass flux between ocean and ice (as it is implemented in the current ice-ocean coupling). 
 \item[\np{nn\_fwb}\forcode{ = 2}]
   freshwater budget is adjusted from the previous year annual mean budget which
@@ -1645 +1720 @@
   the change in the mean sea level at January the first and saved in the \textit{EMPav.dat} file. 
 \end{description}
-
-
 
 % Griffies doc:
@@ -1655 +1728 @@
 % The result of the normalization should be a global integrated zero net water input to the ocean-ice system over 
 % a chosen time scale. 
-%How often the normalization is done is a matter of choice. In mom4p1, we choose to do so at each model time step, 
+% How often the normalization is done is a matter of choice. In mom4p1, we choose to do so at each model time step, 
 % so that there is always a zero net input of water to the ocean-ice system. 
 % Others choose to normalize over an annual cycle, in which case the net imbalance over an annual cycle is used 
@@ -1670 +1743 @@
 % in ocean-ice models. 
 
+
 \biblio
 

@@ -1 @@
-*.aux
-*.bbl
-*.blg
-*.dvi
-*.fdb*
-*.fls
-*.idx
-*.ilg
-*.ind
-*.log
-*.maf
-*.mtc*
-*.out
-*.pdf
-*.toc
-_minted-*
+figures