Index: /NEMO/trunk/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex	(revision 14177)
+++ /NEMO/trunk/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex	(revision 14178)
@@ -46,5 +46,38 @@
 
 \begin{listing}
-  \nlst{namdom_domcfg}
+%  \nlst{namdom_domcfg}
+  \begin{forlines}
+!-----------------------------------------------------------------------
+&namdom        !   space and time domain (bathymetry, mesh, timestep)
+!-----------------------------------------------------------------------
+   nn_bathy    =    1      !  compute analyticaly (=0) or read (=1) the bathymetry file
+                           !  or compute (2) from external bathymetry
+   nn_interp   =    1                          ! type of interpolation (nn_bathy =2)                       
+   cn_topo     =  'bathymetry_ORCA12_V3.3.nc'  ! external topo file (nn_bathy =2)
+   cn_bath     =  'Bathymetry'                 ! topo name in file  (nn_bathy =2)
+   cn_lon      =  'nav_lon'                    ! lon  name in file  (nn_bathy =2)
+   cn_lat      =  'nav_lat'                    ! lat  name in file  (nn_bathy =2)
+   rn_scale    = 1
+   rn_bathy    =    0.     !  value of the bathymetry. if (=0) bottom flat at jpkm1
+   jphgr_msh   =       0               !  type of horizontal mesh
+   ppglam0     =  999999.0             !  longitude of first raw and column T-point (jphgr_msh = 1)
+   ppgphi0     =  999999.0             ! latitude  of first raw and column T-point (jphgr_msh = 1)
+   ppe1_deg    =  999999.0             !  zonal      grid-spacing (degrees)
+   ppe2_deg    =  999999.0             !  meridional grid-spacing (degrees)
+   ppe1_m      =  999999.0             !  zonal      grid-spacing (degrees)
+   ppe2_m      =  999999.0             !  meridional grid-spacing (degrees)
+   ppsur       =   -4762.96143546300   !  ORCA r4, r2 and r05 coefficients
+   ppa0        =     255.58049070440   ! (default coefficients)
+   ppa1        =     245.58132232490   !
+   ppkth       =      21.43336197938   !
+   ppacr       =       3.0             !
+   ppdzmin     =  999999.              !  Minimum vertical spacing
+   pphmax      =  999999.              !  Maximum depth
+   ldbletanh   =  .FALSE.              !  Use/do not use double tanf function for vertical coordinates
+   ppa2        =  999999.              !  Double tanh function parameters
+   ppkth2      =  999999.              !
+   ppacr2      =  999999.              !
+/
+  \end{forlines}
   \caption{\forcode{&namdom_domcfg}}
   \label{lst:namdom_domcfg}
@@ -383,10 +416,39 @@
 \subsubsection[$S$-coordinate (\forcode{ln_sco})]{$S$-coordinate (\protect\np{ln_sco}{ln\_sco})}
 \label{sec:DOMCFG_sco}
+
 \begin{listing}
-  \nlst{namzgr_sco_domcfg}
+%  \nlst{namzgr_sco_domcfg}
   \caption{\forcode{&namzgr_sco_domcfg}}
   \label{lst:namzgr_sco_domcfg}
+  \begin{forlines}
+!-----------------------------------------------------------------------
+&namzgr_sco    !   s-coordinate or hybrid z-s-coordinate                (default: OFF)
+!-----------------------------------------------------------------------
+   ln_s_sh94   = .false.    !  Song & Haidvogel 1994 hybrid S-sigma   (T)|
+   ln_s_sf12   = .false.   !  Siddorn & Furner 2012 hybrid S-z-sigma (T)| if both are false the NEMO tanh stretching is applied
+   ln_sigcrit  = .false.   !  use sigma coordinates below critical depth (T) or Z coordinates (F) for Siddorn & Furner stretch
+                           !  stretching coefficients for all functions
+   rn_sbot_min =   10.0    !  minimum depth of s-bottom surface (>0) (m)
+   rn_sbot_max = 7000.0    !  maximum depth of s-bottom surface (= ocean depth) (>0) (m)
+   rn_hc       =  150.0    !  critical depth for transition to stretched coordinates
+                        !!!!!!!  Envelop bathymetry
+   rn_rmax     =    0.3    !  maximum cut-off r-value allowed (0<r_max<1)
+                        !!!!!!!  SH94 stretching coefficients  (ln_s_sh94 = .true.)
+   rn_theta    =    6.0    !  surface control parameter (0<=theta<=20)
+   rn_bb       =    0.8    !  stretching with SH94 s-sigma
+                        !!!!!!!  SF12 stretching coefficient  (ln_s_sf12 = .true.)
+   rn_alpha    =    4.4    !  stretching with SF12 s-sigma
+   rn_efold    =    0.0    !  efold length scale for transition to stretched coord
+   rn_zs       =    1.0    !  depth of surface grid box
+                           !  bottom cell depth (Zb) is a linear function of water depth Zb = H*a + b
+   rn_zb_a     =    0.024  !  bathymetry scaling factor for calculating Zb
+   rn_zb_b     =   -0.2    !  offset for calculating Zb
+                        !!!!!!!! Other stretching (not SH94 or SF12) [also uses rn_theta above]
+   rn_thetb    =    1.0    !  bottom control parameter  (0<=thetb<= 1)
+/
+  \end{forlines}
 \end{listing}
-Options are defined in \nam{zgr_sco}{zgr\_sco} (\texttt{DOMAINcfg} only).
+
+Options are defined in \forcode{&zgr_sco} (\texttt{DOMAINcfg} only).
 In $s$-coordinate (\np[=.true.]{ln_sco}{ln\_sco}), the depth and thickness of the model levels are defined from
 the product of a depth field and either a stretching function or its derivative, respectively:
Index: /NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex	(revision 14177)
+++ /NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex	(revision 14178)
@@ -372,5 +372,5 @@
 The number of boundary sets is defined by \np{nb_bdy}{nb\_bdy}.
 Each boundary set can be either defined as a series of straight line segments directly in the namelist
-(\np[=.false.]{ln_coords_file}{ln\_coords\_file}, and a namelist block \nam{bdy_index}{bdy\_index} must be included for each set) or read in from a file (\np[=.true.]{ln_coords_file}{ln\_coords\_file}, and a ``\ifile{coordinates.bdy}'' file must be provided).
+(\np[=.false.]{ln_coords_file}{ln\_coords\_file}, and a namelist block \forcode{&nambdy_index} must be included for each set) or read in from a file (\np[=.true.]{ln_coords_file}{ln\_coords\_file}, and a ``\ifile{coordinates.bdy}'' file must be provided).
 The coordinates.bdy file is analagous to the usual \NEMO\ ``\ifile{coordinates}'' file.
 In the example above, there are two boundary sets, the first of which is defined via a file and
@@ -569,8 +569,8 @@
 \autoref{fig:LBC_bdy_geom} shows an example of an irregular boundary.
 
-The boundary geometry for each set may be defined in a namelist nambdy\_index or
+The boundary geometry for each set may be defined in a namelist \forcode{&nambdy_index} or
 by reading in a ``\ifile{coordinates.bdy}'' file.
-The nambdy\_index namelist defines a series of straight-line segments for north, east, south and west boundaries.
-One nambdy\_index namelist block is needed for each boundary condition defined by indexes.
+The \texttt{nambdy\_index} namelist defines a series of straight-line segments for north, east, south and west boundaries.
+One \texttt{nambdy\_index} namelist block is needed for each boundary condition defined by indexes.
 For the northern boundary, \texttt{nbdysegn} gives the number of segments,
 \jp{jpjnob} gives the $j$ index for each segment and \jp{jpindt} and
Index: /NEMO/trunk/doc/latex/NEMO/subfiles/chap_cfgs.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/subfiles/chap_cfgs.tex	(revision 14177)
+++ /NEMO/trunk/doc/latex/NEMO/subfiles/chap_cfgs.tex	(revision 14178)
@@ -243,5 +243,5 @@
 Through \np[=.false.]{ln_read_cfg}{ln\_read\_cfg} in \nam{cfg}{cfg} namelist defined in
 the reference configuration \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}
-analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines.
+analytical definition of grid in GYRE is done in mdl{usrdef\_hrg}, \mdl{usrdef\_zgr} routines.
 Its horizontal resolution (and thus the size of the domain) is determined by
 setting \np{nn_GYRE}{nn\_GYRE} in \nam{usr_def}{usr\_def}: \\
@@ -254,4 +254,18 @@
 see the Configurations pages on the \NEMO\ web site (\NEMO\ Configurations).
 In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:DOM_zgr_e3}).
+
+\begin{listing}
+  \begin{forlines}
+!-----------------------------------------------------------------------
+&namusr_def    !   GYRE user defined namelist  
+!-----------------------------------------------------------------------
+   nn_GYRE     =     1     !  GYRE resolution [1/degrees]
+   ln_bench    = .false.   !  ! =T benchmark with gyre: the gridsize is kept constant
+   jpkglo      =    31     !  number of model levels
+/
+  \end{forlines}
+  \caption{\forcode{&namusr_def}}
+  \label{lst:namusr_def}
+\end{listing}
 
 The GYRE configuration is also used in benchmark test as it is very simple to increase its resolution and
Index: /NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex	(revision 14177)
+++ /NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex	(revision 14178)
@@ -95,5 +95,5 @@
 which imposes a very small time step when an explicit time stepping is used.
 Two methods are proposed to allow a longer time step for the three-dimensional equations:
-the filtered free surface, which is a modification of the continuous equations %(see \autoref{eq:MB_flt?}),
+the filtered free surface, which is a modification of the continuous equations \iffalse (see \autoref{eq:MB_flt?}) \fi ,
 and the split-explicit free surface described below.
 The extra term introduced in the filtered method is calculated implicitly,
