Index: branches/2012/dev_MERGE_2012/DOC/TexFiles/Biblio/Biblio.bib
===================================================================
--- branches/2012/dev_MERGE_2012/DOC/TexFiles/Biblio/Biblio.bib	(revision 3699)
+++ branches/2012/dev_MERGE_2012/DOC/TexFiles/Biblio/Biblio.bib	(revision 3764)
@@ -1412,8 +1412,9 @@
 }
 
-@ARTICLE{Hunke2008,
+@TECHREPORT{Hunke2008,
   author = {E.C. Hunke and W.H. Lipscomb},
   title = {CICE: the Los Alamos sea ice model documentation and software user's manual, 
         Version 4.0},
+  institution = { Los Alamos National Laboratory, N.M.},
   publisher = {LA-CC-06-012, Los Alamos National Laboratory, N.M.},
   year = {2008}
Index: branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_CFG.tex
===================================================================
--- branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_CFG.tex	(revision 3699)
+++ branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_CFG.tex	(revision 3764)
@@ -31,5 +31,5 @@
 
 % ================================================================
-% 1D model functionality
+% 1D model configuration
 % ================================================================
 \section{Water column model: 1D model (C1D) (\key{c1d})}
@@ -48,18 +48,25 @@
 
 The methodology is based on the use of the zoom functionality over the smallest possible 
-domain : a 3 x 3 domain centred on the grid point of interest (see \S\ref{MISC_zoom}), 
+domain : a 3x3 domain centred on the grid point of interest (see \S\ref{MISC_zoom}), 
 with some extra routines. There is no need to define a new mesh, bathymetry, 
 initial state or forcing, since the 1D model will use those of the configuration it is a zoom of. 
-The chosen grid point is set in par\_oce.F90 module by setting the \jp{jpizoom} and \jp{jpjzoom} 
+The chosen grid point is set in \mdl{par\_oce} module by setting the \jp{jpizoom} and \jp{jpjzoom} 
 parameters to the indices of the location of the chosen grid point.
 
-The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero. 
-Therefore a simplified \rou{step} routine is used (\rou{step\_c1d}) in which both lateral tendancy 
-terms and lateral physics are not called, and the vertical velocity is zero (so far, no attempt at
-introducing a Ekman pumping velocity has been made).
-Second, the two components of the velocity are moved on a $T$-point. 
-This requires a specific treatment of the Coriolis term (see \rou{dyncor\_c1d}) and of the 
-dynamic time stepping (\rou{dynnxt\_c1d}).
-All the relevant modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of 
+The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero, and
+second, the two components of the velocity are moved on a $T$-point. 
+Therefore, defining \key{c1d} changes five main things in the code behaviour: 
+\begin{description}
+\item[(1)] the lateral boundary condition routine (\rou{lbc\_lnk}) set the value of the central column 
+of the 3x3 domain is imposed over the whole domain ; 
+\item[(3)] a call to \rou{lbc\_lnk} is systematically done when reading input data ($i.e.$ in \mdl{iom}) ; 
+\item[(3)] a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which 
+both lateral tendancy terms and lateral physics are not called ; 
+\item[(4)] the vertical velocity is zero (so far, no attempt at introducing a Ekman pumping velocity 
+has been made) ; 
+\item[(5)] a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same 
+(see \mdl{dyncor\_c1d}).
+\end{description}
+All the relevant \textit{\_c1d} modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of 
 the \NEMO distribution.
 
@@ -206,5 +213,5 @@
 % -------------------------------------------------------------------------------------------------------------
 \section{GYRE family: double gyre basin (\key{gyre})}
-\label{MISC_config_gyre}
+\label{CFG_gyre}
 
 The GYRE configuration \citep{Levy_al_OM10} have been built to simulated 
Index: branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_DIA.tex
===================================================================
--- branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_DIA.tex	(revision 3699)
+++ branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_DIA.tex	(revision 3764)
@@ -1018,5 +1018,5 @@
 In addition, a series of diagnostics has been added in the \mdl{diaar5}. 
 They corresponds to outputs that are required for AR5 simulations 
-(see Section \ref{MISC_steric} below for one of them). 
+(see Section \ref{DIA_steric} below for one of them). 
 Activating those outputs requires to define the \key{diaar5} CPP key.
 \\
Index: branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_DOM.tex
===================================================================
--- branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_DOM.tex	(revision 3699)
+++ branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_DOM.tex	(revision 3764)
@@ -499,5 +499,5 @@
 Hybridation of the three main coordinates are available: $s-z$ or $s-zps$ coordinate 
 (Fig.~\ref{Fig_z_zps_s_sps}d and \ref{Fig_z_zps_s_sps}e). When using the variable 
-volume option \key{vvl}) ($i.e.$ non-linear free surface), the coordinate follow the 
+volume option \key{vvl} ($i.e.$ non-linear free surface), the coordinate follow the 
 time-variation of the free surface so that the transformation is time dependent: 
 $z(i,j,k,t)$ (Fig.~\ref{Fig_z_zps_s_sps}f). This option can be used with full step 
Index: branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_DYN.tex
===================================================================
--- branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_DYN.tex	(revision 3699)
+++ branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_DYN.tex	(revision 3764)
@@ -127,5 +127,5 @@
 This is of paramount importance. Replacing $T$ by the number $1$ in the tracer equation and summing
 over the water column must lead to the sea surface height equation otherwise tracer content
-will not be conserved \ref{Griffies_al_MWR01, LeclairMadec2009}.
+will not be conserved \citep{Griffies_al_MWR01, Leclair_Madec_OM09}.
 
 The vertical velocity is computed by an upward integration of the horizontal 
@@ -189,5 +189,5 @@
 the relative vorticity term and horizontal kinetic energy for the planetary vorticity 
 term (MIX scheme) ; or conserving both the potential enstrophy of horizontally non-divergent 
-flow and horizontal kinetic energy (EEN scheme) (see  Appendix~\ref{Apdx_C_vor_zad}). In the 
+flow and horizontal kinetic energy (EEN scheme) (see  Appendix~\ref{Apdx_C_vorEEN}). In the 
 case of ENS, ENE or MIX schemes the land sea mask may be slightly modified to ensure the 
 consistency of vorticity term with analytical equations (\textit{ln\_dynvor\_con}=true).
@@ -331,5 +331,5 @@
 This EEN scheme in fact combines the conservation properties of the ENS and ENE schemes. 
 It conserves both total energy and potential enstrophy in the limit of horizontally 
-nondivergent flow ($i.e.$ $\chi$=$0$) (see  Appendix~\ref{Apdx_C_vor_zad}). 
+nondivergent flow ($i.e.$ $\chi$=$0$) (see  Appendix~\ref{Apdx_C_vorEEN}). 
 Applied to a realistic ocean configuration, it has been shown that it leads to a significant 
 reduction of the noise in the vertical velocity field \citep{Le_Sommer_al_OM09}. 
@@ -938,5 +938,5 @@
 is the \textit{before} velocity in time, except for the pure vertical component 
 that appears when a tensor of rotation is used. This latter term is solved 
-implicitly together with the vertical diffusion term (see \S\ref{DOM_nxt}) 
+implicitly together with the vertical diffusion term (see \S\ref{STP}) 
 
 At the lateral boundaries either free slip, no slip or partial slip boundary 
@@ -1066,5 +1066,5 @@
 scheme (\np{ln\_zdfexp}=true) using a time splitting technique 
 (\np{nn\_zdfexp} $>$ 1) or $(b)$ a backward (or implicit) time differencing scheme 
-(\np{ln\_zdfexp}=false) (see \S\ref{DOM_nxt}). Note that namelist variables 
+(\np{ln\_zdfexp}=false) (see \S\ref{STP}). Note that namelist variables 
 \np{ln\_zdfexp} and \np{nn\_zdfexp} apply to both tracers and dynamics. 
 
Index: branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_TRA.tex
===================================================================
--- branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_TRA.tex	(revision 3699)
+++ branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_TRA.tex	(revision 3764)
@@ -264,5 +264,5 @@
 transport) rather than TVD. The TVD scheme is implemented in the \mdl{traadv\_tvd} module.
 
-For stability reasons (see \S\ref{DOM_nxt}),
+For stability reasons (see \S\ref{STP}),
 $\tau _u^{cen2}$ is evaluated  in (\ref{Eq_tra_adv_tvd}) using the \textit{now} tracer while $\tau _u^{ups}$ 
 is evaluated using the \textit{before} tracer. In other words, the advective part of 
@@ -337,5 +337,5 @@
 \np{ln\_traadv\_ubs}=true.
 
-For stability reasons  (see \S\ref{DOM_nxt}),
+For stability reasons  (see \S\ref{STP}),
 the first term  in \eqref{Eq_tra_adv_ubs} (which corresponds to a second order centred scheme) 
 is evaluated using the \textit{now} tracer (centred in time) while the 
@@ -451,5 +451,5 @@
 except for the pure vertical component that appears when a rotation tensor 
 is used. This latter term is solved implicitly together with the 
-vertical diffusion term (see \S\ref{DOM_nxt}).
+vertical diffusion term (see \S\ref{STP}).
 
 % -------------------------------------------------------------------------------------------------------------
Index: branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_ZDF.tex
===================================================================
--- branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_ZDF.tex	(revision 3699)
+++ branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_ZDF.tex	(revision 3764)
@@ -120,5 +120,5 @@
 \end{equation}
 
-is computed from the wind stress vector $|\tau|$ and the reference dendity $ \rho_o$.
+is computed from the wind stress vector $|\tau|$ and the reference density $ \rho_o$.
 The final $h_{e}$ is further constrained by the adjustable bounds \np{rn\_mldmin} and \np{rn\_mldmax}.
 Once $h_{e}$ is computed, the vertical eddy coefficients within $h_{e}$ are set to 
@@ -1188,5 +1188,5 @@
 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_ZDF_M2_K1_tmx.pdf}
 \caption{  \label{Fig_ZDF_M2_K1_tmx} 
-(a) M2 and (b) K2 internal wave drag energy from \citet{Carrere_Lyard_GRL03} ($W/m^2$). }
+(a) M2 and (b) K1 internal wave drag energy from \citet{Carrere_Lyard_GRL03} ($W/m^2$). }
 \end{center}  	\end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
@@ -1205,5 +1205,5 @@
 
 When \np{ln\_tmx\_itf}=true, the two key parameters $q$ and $F(z)$ are adjusted following 
-the parameterisation developed by \ref{Koch-Larrouy_al_GRL07}:
+the parameterisation developed by \citet{Koch-Larrouy_al_GRL07}:
 
 First, the Indonesian archipelago is a complex geographic region 
@@ -1219,5 +1219,5 @@
 Second, the vertical structure function, $F(z)$, is no more associated
 with a bottom intensification of the mixing, but with a maximum of 
-energy available within the thermocline. \ref{Koch-Larrouy_al_GRL07} 
+energy available within the thermocline. \citet{Koch-Larrouy_al_GRL07} 
 have suggested that the vertical distribution of the energy dissipation 
 proportional to $N^2$ below the core of the thermocline and to $N$ above. 
@@ -1236,5 +1236,5 @@
 and vertical distributions of the mixing are adequately prescribed 
 \citep{Koch-Larrouy_al_GRL07, Koch-Larrouy_al_OD08a, Koch-Larrouy_al_OD08b}.
-Note also that such a parameterisation has a sugnificant impact on the behaviour 
+Note also that such a parameterisation has a significant impact on the behaviour 
 of global coupled GCMs \citep{Koch-Larrouy_al_CD10}.
 
Index: branches/2012/dev_MERGE_2012/DOC/TexFiles/Namelist/namasm
===================================================================
--- branches/2012/dev_MERGE_2012/DOC/TexFiles/Namelist/namasm	(revision 3699)
+++ branches/2012/dev_MERGE_2012/DOC/TexFiles/Namelist/namasm	(revision 3764)
@@ -3,5 +3,4 @@
 !-----------------------------------------------------------------------
     ln_bkgwri = .false.    !  Logical switch for writing out background state 
-    ln_trjwri = .false.    !  Logical switch for writing out state trajectory
     ln_trainc = .false.    !  Logical switch for applying tracer increments
     ln_dyninc = .false.    !  Logical switch for applying velocity increments
@@ -14,5 +13,4 @@
     nitiaufin = 15         !  Timestep of end of IAU interval in [0,nitend-nit000-1]
     niaufn    = 0          !  Type of IAU weighting function
-    nittrjfrq = 0          !  Frequency of trajectory output for 4D-VAR
     ln_salfix = .false.    !  Logical switch for ensuring that the sa > salfixmin
     salfixmin = -9999      !  Minimum salinity after applying the increments
Index: branches/2012/dev_MERGE_2012/DOC/TexFiles/Namelist/namdyn_vor
===================================================================
--- branches/2012/dev_MERGE_2012/DOC/TexFiles/Namelist/namdyn_vor	(revision 3699)
+++ branches/2012/dev_MERGE_2012/DOC/TexFiles/Namelist/namdyn_vor	(revision 3764)
@@ -2,6 +2,6 @@
 &namdyn_vor    !   option of physics/algorithm (not control by CPP keys)
 !-----------------------------------------------------------------------
-   ln_dynvor_ene = .false. !  enstrophy conserving scheme  
-   ln_dynvor_ens = .false. !  energy conserving scheme    
+   ln_dynvor_ene = .false. !  energy    conserving scheme  
+   ln_dynvor_ens = .false. !  enstrophy conserving scheme    
    ln_dynvor_mix = .false. !  mixed scheme               
    ln_dynvor_een = .true.  !  energy & enstrophy scheme  
