Changeset 2349 for branches/nemo_v3_3_beta/DOC/TexFiles

branches/nemo_v3_3_beta/DOC/TexFiles/Biblio/Biblio.bib

-                      r2298
+                      r2349
 @ARTICLE{Boulanger_al_GRL01,
   author = {J.-P. Boulanger and E. Durand and J.-P. Duvel and C. Menkes and P.
    Delecluse and M. Imbard and M. Lengaigne and G.Madec and S. Masson},
+   Delecluse and M. Imbard and M. Lengaigne and G. Madec and S. Masson},
   title = {Role of non-linear oceanic processes in the response to westerly
    wind events: new implications for the 1997 El Niño onset},
 …
   pages = {1603--1606}
+}
+@ARTICLE{Brodeau_al_OM09,
+  author = {L. Brodeau and B. Barnier and A.-M. Tr\'{e}guier and T. Penduff and S. Gulev},
+  title = {An ERA40-based atmospheric forcing for global ocean circulation models},
+  journal = OM,
+  year = {2009},
+  volume = {31},  number = {3-4},
+  pages = {88--104}
+}
 @ARTICLE{de_Boyer_Montegut_al_JGR04,
 …
+}
+@ARTICLE{Drijfhout_JPO94,
+  author = {S. S. Drijfhout},
+  title = {Heat transport by Mesoscale Eddies in an Ocean Circulation Model},
+  journal = JPO,
+  year = {1994},
+  volume = {24},
+  pages = {353--369}
+}
 @ARTICLE{Dukowicz1994,
   author = {J. K. Dukowicz and R. D. Smith},
 …
 @ARTICLE{D'Ortenzio_al_GRL05,
   author = {F. D’Ortenzio and D. Iudicone and C. de Boyer Mont\'{e}gut and P.
+  author = {F. D\'Ortenzio and D. Iudicone and C. de Boyer Mont\'{e}gut and P.
    Testor and D. Antoine and S. Marullo and R. Santoleri and G. Madec},
   title = {Seasonal variability of the mixed layer depth in the Mediterranean
 …
+}
+@ARTICLE{Hazeleger_Drijfhout_JPO98,
+  author = {W. Hazeleger and S. S. Drijfhout},
+  title = {Mode water variability in a model of the subtropical gyre: response to anomalous forcing},
+  journal = JPO,
+  year = {1998},
+  volume = {28},
+  pages = {266--288},
+}
+@ARTICLE{Hazeleger_Drijfhout_JPO99,
+  author = {W. Hazeleger and S. S. Drijfhout},
+  title = {Stochastically forced mode water variability},
+  journal = JPO,
+  year = {1999},
+  volume = {29},
+  pages = {1772--1786},
+}
+@ARTICLE{Hazeleger_Drijfhout_JGR00,
+  author = {W. Hazeleger and S. S. Drijfhout},
+  title = {A model study on internally generated variability in subtropical mode water formation},
+  journal = JGR,
+  year = {2000},
+  volume = {105},
+  pages = {13,965--13,979},
+}
+@ARTICLE{Hazeleger_Drijfhout_JPO00,
+  author = {W. Hazeleger and S. S. Drijfhout},
+  title = {Eddy subduction in a model of the subtropical gyre},
+  journal = JPO,
+  year = {2000},
+  volume = {30},
+  pages = {677--695},
+}
 @ARTICLE{Hirt_al_JCP74,
   author = {C. W. Hirt and A. A. Amsden and J. L. Cook},
 …
+}
 @ARTICLE{Levy_al_JGR10,
+@ARTICLE{Levy_al_OM10,
   author = {M. L\'{e}vy and P. Klein and A.-M. Tr\'{e}guier and D. Iovino and
    G. Madec and S. Masson and T. Takahashi},
   title = {Impacts of sub-mesoscale physics on idealized gyres},
   journal = JGR,
+  journal = OM,
   year = {2010},
   volume = {34},  number = {1-2},
 …
 @ARTICLE{Levy_al_DSR00,
   author = {M. L\'{e}vy and L. Mémery and G. Madec},
+  author = {M. L\'{e}vy and L. M\'{e}mery and G. Madec},
   title = {Combined effects of mesoscale processes and atmospheric high-frequency
    variability on the spring bloom in the MEDOC area},
 …
   publisher = {NCAR Technical Note, NCAR/TN-460+STR, CGD Division of the National Center for Atmospheric Research},
   year = {2004},
   author = {W. Large and S. Yeager}}
+  author = {W. G. Large and S. Yeager}}
 @ARTICLE{Large_al_RG94,
 …
   doi = {10.1016/j.ocemod.2009.06.006},
   url = {http://dx.doi.org/}
+}
+@ARTICLE{Leclair_Madec_OM10s,
+  author = {M. Leclair and G. Madec},
+  title = {$\tilde{z}$-coordinate, an Arbitrary Lagrangian-Eulerian coordinate separating high and low frequency},
+  journal = OM,
+  year = {2010},
+  pages = {submitted},
+}
 …
 @ARTICLE{Timmermann_al_OM05,
   author = {R. Timmermann and H. Goosse and G. Madec and T. Fichefet, and C. \'{E}the and V. Duli\`{e}re},
+  author = {R. Timmermann and H. Goosse and G. Madec and T. Fichefet and C. \'{E}the and V. Duli\`{e}re},
   title = {On the representation of high latitude processes in the ORCA-LIM global coupled sea ice-ocean model},
   journal = OM,

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Annex_D.tex

-                      r2282
+                      r2349
 \end{table}
 %--------------------------------------------------------------------------------------------------------------
+\newpage
+% ================================================================
+% The program structure
+% ================================================================
+\section{The program structure}
+\label{Apdx_D_structure}

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_ASM.tex

-                      r2298
+                      r2349
 temperature, salinity, sea surface height, velocity and sea ice concentration.
 These are read into the model from a file which may be produced by data assimilation.
 This code is controlled by the namelist \np{nam\_asminc}.
+This code is controlled by the namelist \textit{nam\_asminc}.
 There is a brief description of all the namelist options provided.
 To build the ASM code \np{key\_asminc} must be set.
+To build the ASM code \key{asminc} must be set.
 %===============================================================
+\subsection{Direct initialization}
+\section{Direct initialization}
+\label{ASM_DI}
 Direct initialization refers to the instantaneous correction
+Direct initialization (DI) refers to the instantaneous correction
 of the model background state using the analysis increment.
+DI is used when \np{ln\_asmdin} is set to true.
+\subsection{Incremental Analysis Updates}
+\section{Incremental Analysis Updates}
+\label{ASM_IAU}
 Rather than updating the model state directly with the analysis increment,
 …
 is referred to as Incremental Analysis Updates (IAU) \citep{Bloom_al_MWR96}.
 IAU is a common technique used with 3D assimilation methods such as 3D-Var or OI.
+IAU is used when \np{ln\_asmiau} is set to true.
 With IAU, the model state trajectory in the assimilation window
 …
 for temperature, salinity, horizontal velocity and SSH
 as additional tendency terms to the prognostic equations:
 \begin{eqnarray}
+\begin{eqnarray}     \label{eq:wa_traj_iau}
 {\bf x}^{a}(t_{i}) = M(t_{i}, t_{0})[{\bf x}^{b}(t_{0})]
 \; + \; F_{i} \delta \tilde{\bf x}^{a}
-\label{eq:wa_traj_iau}
 \end{eqnarray}
 where $F_{i}$ is a weighting function defined such that $\sum_{i=1}^{N} F_{i}=1$.
 …
 In addition, two different weighting functions have been implemented.
 The first function employs constant weights,
 \begin{eqnarray}
+\begin{eqnarray}    \label{eq:F1_i}
 F^{(1)}_{i}
 =\left\{ \begin{array}{ll}
+   &
+   {\rm if} \; \; \; t_{i} < t_{m} \\
+/M &
+   {\rm if} \; \; \; t_{m} < t_{i} \leq t_{n} \\
+  &
+   {\rm if} \; \; \; t_{i} > t_{n}
+     &    {\rm if} \; \; \; t_{i} < t_{m}                \\
+/M &    {\rm if} \; \; \; t_{m} < t_{i} \leq t_{n} \\
+     &    {\rm if} \; \; \; t_{i} > t_{n}
   \end{array} \right.
-\label{eq:F1_i}
 \end{eqnarray}
 where $M = m-n$.
 …
 weight in the centre of the sub-window, with the weighting reduced
 linearly to a small value at the window end-points.
 \begin{eqnarray}
+\begin{eqnarray}     \label{eq:F2_i}
 F^{(2)}_{i}
 =\left\{ \begin{array}{ll}
+   &
+   {\rm if} \; \; \; t_{i} < t_{m} \\
+   \alpha \, i &
+   {\rm if} \; \; \; t_{m} \leq t_{i} \leq t_{M/2} \\
+   \alpha \, (M - i +1) &
+   {\rm if} \; \; \; t_{M/2} < t_{i} \leq t_{n} \\
+  &
+   {\rm if} \; \; \; t_{i} > t_{n}
+                           &    {\rm if} \; \; \; t_{i}       <     t_{m}                        \\
+   \alpha \, i               &    {\rm if} \; \; \; t_{m}    \leq t_{i}    \leq   t_{M/2}   \\
+   \alpha \, (M - i +1) &    {\rm if} \; \; \; t_{M/2}  <    t_{i}    \leq   t_{n}       \\
+                            &   {\rm if} \; \; \; t_{i}        >    t_{n}
   \end{array} \right.
-\label{eq:F2_i}
 \end{eqnarray}
 where $\alpha^{-1} = \sum_{i=1}^{M/2} 2i$ and $M$ is assumed to be even.
 The weights described by Eq.~(\ref{eq:F2_i}) provide a
+The weights described by \eqref{eq:F2_i} provide a
 smoother transition of the analysis trajectory from one assimilation cycle
 to the next than that described by Eq.~(\ref{eq:F1_i}).
+to the next than that described by \eqref{eq:F1_i}.
 %==========================================================================
 …
 %-------------------------------------------------------------------------------------------------------------
+\subsection{Assimilation increments file}
+The header of an assimilation increments file produced using \np{ncdump -h} is shown below
+The header of an assimilation increments file produced using \textit{ncdump~-h} is shown below
 \begin{alltt}

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_DOM.tex

-                      r2285
+                      r2349
 option which can be enabled or disabled in the middle of an experiment. Three main
 choices are offered (Fig.~\ref{Fig_z_zps_s_sps}a to c): $z$-coordinate with full step
 bathymetry (\np{ln\_zco}=true), $z$-coordinate with partial step bathymetry
 (\np{ln\_zps}=true), or generalized, $s$-coordinate (\np{ln\_sco}=true).
+bathymetry (\np{ln\_zco}~=~true), $z$-coordinate with partial step bathymetry
+(\np{ln\_zps}~=~true), or generalized, $s$-coordinate (\np{ln\_sco}~=~true).
 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
 …
 \namdisplay{namzgr_sco}
 %--------------------------------------------------------------------------------------------------------------
 In $s$-coordinate (\key{sco} is defined), the depth and thickness of the model
+In $s$-coordinate (\np{ln\_sco}~=~true), 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:

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_DYN.tex

-                      r2285
+                      r2349
 equation and the associated barotropic velocity equations with a smaller time
 step than $\rdt$, the time step used for the three dimensional prognostic
 variables (Fig.\ref {Fig_DYN_dynspg_ts}).
 The size of the small time step, $\Delta_e$ (the external mode or barotropic time step)
+variables (Fig.~\ref{Fig_DYN_dynspg_ts}).
+The size of the small time step, $\rdt_e$ (the external mode or barotropic time step)
  is provided through the \np{nn\_baro} namelist parameter as:
 $\Delta_e = \Delta / nn\_baro$.
+$\rdt_e = \rdt / nn\_baro$.
 …
 the time averaged vertically integrated transport. Notably, there is no Robert-Asselin time filter used in the barotropic portion of the integration.
 Upon reaching $t_{n=N} = \tau + 2\Delta \tau$ , the vertically integrated velocity is time averaged to produce the updated vertically integrated velocity at baroclinic time $\tau + \Delta \tau$
+Upon reaching $t_{n=N} = \tau + 2\rdt \tau$ , the vertically integrated velocity is time averaged to produce the updated vertically integrated velocity at baroclinic time $\tau + \rdt \tau$
 \begin{equation} \label{DYN_spg_ts_u}
 \textbf{U}(\tau+\rdt) = \overline{\textbf{U}^{(b)}(\tau+\rdt)}
 …
 and Asselin filtering is done in \mdl{dynnxt}.
+% ================================================================
+% ================================================================

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_LBC.tex

-                      r2282
+                      r2349
 % Open Boundary Conditions
 % ================================================================
 \section{Open Boundary Conditions (\key{obc})}
+\section{Open Boundary Conditions (\key{obc}) (OBC)}
 \label{LBC_obc}
 %-----------------------------------------nam_obc  -------------------------------------------
 …
 % Unstructured open boundaries BDY
 % ====================================================================
 \section{Unstructured Open Boundary Conditions (\key{bdy})}
+\section{Unstructured Open Boundary Conditions (\key{bdy}) (BDY)}
 \label{LBC_bdy}
 %-----------------------------------------nambdy--------------------------------------------
+%-    filbdy_mask    =  ''                  !  name of mask file (if ln_bdy_mask=.TRUE.)
+%-    filbdy_data_T  = 'bdydata_grid_T.nc'  !  name of data file for FRS condition (T-points)
+%-    filbdy_data_U  = 'bdydata_grid_U.nc'  !  name of data file for FRS condition (U-points)
+%-    filbdy_data_V  = 'bdydata_grid_V.nc'  !  name of data file for FRS condition (V-points)
+%-    filbdy_data_bt_T  = 'bdydata_bt_grid_T.nc'  !  name of data file for Flather condition (T-points)
+%-    filbdy_data_bt_U  = 'bdydata_bt_grid_U.nc'  !  name of data file for Flather condition (U-points)
+%-    filbdy_data_bt_V  = 'bdydata_bt_grid_V.nc'  !  name of data file for Flather condition (V-points)
+%-    ln_bdy_clim    = .false.              !  contain 1 (T) or 12 (F) time dumps and be cyclic
+%-    ln_bdy_vol     = .true.               !  total volume correction (see volbdy parameter)
+%-    ln_bdy_mask    = .false.              !  boundary mask from filbdy_mask (T) or boundaries are on edges of domain (F)
+%-    ln_bdy_tides   = .true.               !  Apply tidal harmonic forcing with Flather condition
+%-    ln_bdy_dyn_fla = .true.               !  Apply Flather condition to velocities
+%-    ln_bdy_tra_frs = .false.              !  Apply FRS condition to temperature and salinity
+%-    ln_bdy_dyn_frs = .false.              !  Apply FRS condition to velocities
+%-    nbdy_dta       =  1                   !  = 0, bdy data are equal to the initial state
+%-                                          !  = 1, bdy data are read in 'bdydata   .nc' files
+%-    nb_rimwidth    = 9                    !  width of the relaxation zone
+%-    volbdy         = 0                    !  = 0, the total water flux across open boundaries is zero
+%-    cn_mask    =  ''                        !  name of mask file (if ln_bdy_mask=.TRUE.)
+%-    cn_dta_frs_T  = 'bdydata_grid_T.nc'     !  name of data file (T-points)
+%-    cn_dta_frs_U  = 'bdydata_grid_U.nc'     !  name of data file (U-points)
+%-    cn_dta_frs_V  = 'bdydata_grid_V.nc'     !  name of data file (V-points)
+%-    cn_dta_fla_T  = 'bdydata_bt_grid_T.nc'  !  name of data file for Flather condition (T-points)
+%-    cn_dta_fla_U  = 'bdydata_bt_grid_U.nc'  !  name of data file for Flather condition (U-points)
+%-    cn_dta_fla_V  = 'bdydata_bt_grid_V.nc'  !  name of data file for Flather condition (V-points)
+%-    ln_clim    = .false.                    !  contain 1 (T) or 12 (F) time dumps and be cyclic
+%-    ln_vol     = .true.                     !  total volume correction (see volbdy parameter)
+%-    ln_mask    = .false.                    !  boundary mask from filbdy_mask (T) or boundaries are on edges of domain (F)
+%-    ln_tides   = .true.                     !  Apply tidal harmonic forcing with Flather condition
+%-    ln_dyn_fla = .true.                     !  Apply Flather condition to velocities
+%-    ln_tra_frs = .false.                    !  Apply FRS condition to temperature and salinity
+%-    ln_dyn_frs = .false.                    !  Apply FRS condition to velocities
+%-    nn_rimwidth    =  9                     !  width of the relaxation zone
+%-    nn_dtactl      =  1                     !  = 0, bdy data are equal to the initial state
+%-                                            !  = 1, bdy data are read in 'bdydata   .nc' files
+%-    nn_volctl      =  0                     !  = 0, the total water flux across open boundaries is zero
+%-                                            !  = 1, the total volume of the system is conserved
 \namdisplay{nambdy}
 %-----------------------------------------------------------------------------------------------
 …
 \end{equation}
 The width of the FRS zone is specified in the namelist as
 \np{nb\_rimwidth}. This is typically set to a value between 8 and 10.
+\np{nn\_rimwidth}. This is typically set to a value between 8 and 10.
 %----------------------------------------------
 …
 The Flow Relaxation Scheme may be applied separately to the
 temperature and salinity (\np{ln\_bdy\_tra\_frs} = true) and
 the velocity fields (\np{ln\_bdy\_dyn\_frs} = true). Flather
+temperature and salinity (\np{ln\_tra\_frs} = true) and
+the velocity fields (\np{ln\_dyn\_frs} = true). Flather
 radiation conditions may be applied using externally defined
 barotropic velocities and sea-surface height (\np{ln\_bdy\_dyn\_fla} = true)
 or using tidal harmonics fields (\np{ln\_bdy\_tides} = true)
+barotropic velocities and sea-surface height (\np{ln\_dyn\_fla} = true)
+or using tidal harmonics fields (\np{ln\_tides} = true)
 or both. FRS and Flather conditions may be applied simultaneously.
 A typical configuration where all possible conditions might be used is a tidal,
 …
 The input data files for the FRS conditions are defined in the
 namelist as \np{filbdy\_data\_T}, \np{filbdy\_data\_U},
 \np{filbdy\_data\_V}. The input data files for the Flather conditions
 are defined in the namelist as \np{filbdy\_data\_bt\_T},
 \np{filbdy\_data\_bt\_U}, \np{filbdy\_data\_bt\_V}.
 The netcdf header of a typical input data file is shown in Figure
+\ref{Fig_LBC_nc_header}. The file contains the index arrays which
+define the boundary geometry as noted above and the data arrays for
+each field.  The data arrays are dimensioned on: a time
+dimension; $xb$ which is the index of the boundary data point in the
 horizontal; and $yb$ which is a degenerate dimension of 1 to enable
+namelist as \np{cn\_dta\_frs\_T}, \np{cn\_dta\_frs\_U},
+\np{cn\_dta\_frs\_V}. The input data files for the Flather conditions
+are defined in the namelist as \np{cn\_dta\_fla\_T},
+\np{cn\_dta\_fla\_U}, \np{cn\_dta\_fla\_V}.
+The netcdf header of a typical input data file is shown in Fig.~\ref{Fig_LBC_nc_header}.
+The file contains the index arrays which define the boundary geometry
+as noted above and the data arrays for each field.
+The data arrays are dimensioned on: a time dimension; $xb$
+which is the index of the boundary data point in the horizontal;
+and $yb$ which is a degenerate dimension of 1 to enable
 the file to be read by the standard NEMO I/O routines. The 3D fields
 also have a depth dimension.
 If \np{ln\_bdy\_clim} is set to $false$, the model expects the
+If \np{ln\_clim} is set to \textit{false}, the model expects the
 units of the time axis to have the form shown in
 \ref{Fig_bdy_input_file}, $i.e.$ {\it ``seconds since yyyy-mm-dd
+Fig.~\ref{Fig_LBC_nc_header}, $i.e.$ {\it ``seconds since yyyy-mm-dd
 hh:mm:ss''} The fields are then linearly interpolated to the model
 time at each timestep. Note that for this option, the time axis of the
 input files must completely span the time period of the model
 integration. If \np{ln\_bdy\_clim} is set to $.true.$ (climatological
+integration. If \np{ln\_clim} is set to \textit{true} (climatological
 boundary forcing), the model will expect either a single set of annual
 mean fields (constant boundary forcing) or 12 sets of monthly mean
 …
 As in the OBC module there is an option to use initial conditions as
 boundary conditions. This is chosen by setting
 $\np{nb\_dta}=0$. However, since the model defines the boundary
+\np{nn\_dtactl}~=~0. However, since the model defines the boundary
 geometry by reading the boundary index arrays from the input files,
 it is still necessary to provide a set of input files in this
 case. They need only contain the boundary index arrays, $nbidta$,
 $nbjdta$, $nbrdta$.
+\textit{nbjdta}, \textit{nbrdta}.
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 …
 \label{BDY_vol_corr}
+There is an option to force the total volume in the regional model to be constant, similar to the option in the OBC module. This is controlled  by the \np{volbdy} parameter in the namelist. A value of $\np{volbdy} = 0$ indicates that this option is not used. If  $\np{volbdy} = 1$ then a correction is applied to the normal velocities around the boundary at each timestep to ensure that the integrated volume flow through the boundary is zero. If $\np{volbdy} = 2$ then the calculation of the volume change on the timestep includes the change due to the freshwater flux across the surface and the correction velocity corrects for this as well.
+There is an option to force the total volume in the regional model to be constant,
+similar to the option in the OBC module. This is controlled  by the \np{nn\_volctl}
+parameter in the namelist. A value of\np{nn\_volctl}~=~0 indicates that this option is not used.
+If  \np{nn\_volctl}~=~1 then a correction is applied to the normal velocities
+around the boundary at each timestep to ensure that the integrated volume flow
+through the boundary is zero. If \np{nn\_volctl}~=~2 then the calculation of
+the volume change on the timestep includes the change due to the freshwater
+flux across the surface and the correction velocity corrects for this as well.

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_LDF.tex

-                      r2282
+                      r2349
 The specification of the space variation of the coefficient is made in
 \mdl{ldftra} and \mdl{ldfdyn}, or more precisely in include files
 \textit{ldftra\_cNd.h90} and \textit{ldfdyn\_cNd.h90}, with N=1, 2 or 3.
+\textit{traldf\_cNd.h90} and \textit{dynldf\_cNd.h90}, with N=1, 2 or 3.
 The user can modify these include files as he/she wishes. The way the
 mixing coefficient are set in the reference version can be briefly described
 …
 \subsubsection{Constant Mixing Coefficients (default option)}
 When none of the \textbf{key\_ldfdyn\_...} and \textbf{key\_ldftra\_...} keys are
+When none of the \textbf{key\_dynldf\_...} and \textbf{key\_traldf\_...} keys are
 defined, a constant value is used over the whole ocean for momentum and
 tracers, which is specified through the \np{rn\_ahm0} and \np{rn\_aht0} namelist
 parameters.
 \subsubsection{Vertically varying Mixing Coefficients (\key{ldftra\_c1d} and \key{ldfdyn\_c1d})}
+\subsubsection{Vertically varying Mixing Coefficients (\key{traldf\_c1d} and \key{dynldf\_c1d})}
 The 1D option is only available when using the $z$-coordinate with full step.
 Indeed in all the other types of vertical coordinate, the depth is a 3D function
 …
 and the transition takes place around z=300~m with a width of 300~m
 ($i.e.$ both the depth and the width of the inflection point are set to 300~m).
 This profile is hard coded in file \hf{ldftra\_c1d}, but can be easily modified by users.
 \subsubsection{Horizontally Varying Mixing Coefficients (\key{ldftra\_c2d} and \key{ldfdyn\_c2d})}
+This profile is hard coded in file \hf{traldf\_c1d}, but can be easily modified by users.
+\subsubsection{Horizontally Varying Mixing Coefficients (\key{traldf\_c2d} and \key{dynldf\_c2d})}
 By default the horizontal variation of the eddy coefficient depends on the local mesh
 size and the type of operator used:
 …
 defined, see \hf{ldfdyn\_antarctic} and \hf{ldfdyn\_arctic}).
 \subsubsection{Space Varying Mixing Coefficients (\key{ldftra\_c3d} and \key{ldfdyn\_c3d})}
+\subsubsection{Space Varying Mixing Coefficients (\key{traldf\_c3d} and \key{dynldf\_c3d})}
 The 3D space variation of the mixing coefficient is simply the combination of the
 …
 spurious diapycnal diffusion (see {\S\ref{LDF_slp}).
 (4) when an eddy induced advection term is used (\key{trahdf\_eiv}), $A^{eiv}$,
+(4) when an eddy induced advection term is used (\key{traldf\_eiv}), $A^{eiv}$,
 the eddy induced coefficient has to be defined. Its space variations are controlled
 by the same CPP variable as for the eddy diffusivity coefficient ($i.e.$

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_MISC.tex

-                      r2282
+                      r2349
 Mediterranean to replenish its supply of water from the Atlantic to balance the net
 evaporation occurring over the Mediterranean region. This problem occurs even in
 eddy permitting simulations. For example, in ORCA 1/4\r{} several straits of the Indonesian
+eddy permitting simulations. For example, in ORCA 1/4\deg several straits of the Indonesian
 archipelago (Ombai, Lombok...) are much narrow than even a single ocean grid-point.
 …
 Note that such modifications are so specific to a given configuration that no attempt
 has been made to set them in a generic way. However, examples of how
 they can be set up is given in the ORCA 2\r{} and 0.5\r{} configurations (search for
 \key{ORCA\_R2} or \key{ORCA\_R05} in the code).
+they can be set up is given in the ORCA 2\deg and 0.5\deg configurations (search for
+\key{orca\_r2} or \key{orca\_r05} in the code).
 % -------------------------------------------------------------------------------------------------------------
 …
 \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_Gibraltar.pdf}
 \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_Gibraltar2.pdf}
 \caption {Example of the Gibraltar strait defined in a 1\r{} x 1\r{} mesh.
+\caption {Example of the Gibraltar strait defined in a $1\deg \times 1\deg$ mesh.
 \textit{Top}: using partially open cells. The meridional scale factor at $v$-point
 is reduced on both sides of the strait to account for the real width of the strait
 …
 % 1D model functionality
 % ================================================================
 \section{Water column model: 1D model (\key{cfg\_1d})}
+\section{Water column model: 1D model (\key{c1d})}
 \label{MISC_1D}
 The 1D model option simulates a stand alone water column within the 3D \NEMO system.
 It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers
 or a biogeochemical model. It is set up by defining the \key{cfg\_1d} CPP key.
+or a biogeochemical model. It is set up by defining the \key{c1d} CPP key.
 The 1D model is a very useful tool
 \textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes ;
 …
 % \gmcomment{why not make these bullets into subsections?}
+Three issues to be described here:
+$\bullet$ Vector and memory optimisation:
+$\bullet$ Vector optimisation:
 \key{vectopt\_loop} enables the internal loops to collapse. This is very
 …
 % Add also one word on NEC specific optimisation (Novercheck option for example)
-\key{vectopt\_memory} is an obsolescent option. It has been introduced in order
-to reduce the memory requirement of the model at a time when in-core memory
-were rather limited. This is obviously done at the cost of increasing the CPU
-time requirement, since it suppress intermediate computations which would have
-been saved in in-core memory. Currently it is only used in the old implementation
-of the TKE physics (\key{tke\_old}) where,  when \key{vectopt\_memory}
-is defined, the coefficients used for horizontal smoothing of $A_v^T$ and $A_v^m$
-are no longer computed once and for all. This reduces the memory requirement by three
-D arrays. This option will disappear in the next \NEMO release.
 $\bullet$ Control print %: describe here 4 things:
 …
 % Diagnostics
 % ================================================================
 \section{Diagnostics (DIA, IOM)}
+\section{Diagnostics (DIA, IOM, TRD, FLO)}
 \label{MISC_diag}
 …
 %       Standard Model Output
 % -------------------------------------------------------------------------------------------------------------
 \subsection{Standard Model Output (default option or \key{dimg})}
+\subsection{Model Output (default or \key{iomput} or \key{dimgout})}
 \label{MISC_iom}
 …
 flexibility in the choice of the fields to be output as well as how the
 writing work is distributed over the processors in massively parallel
 computing. It is activated when \key{dimgout} is defined.
+computing. It is activated when \key{iomput} is defined.
 % -------------------------------------------------------------------------------------------------------------
 %       Tracer/Dynamics Trends
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Tracer/Dynamics Trends (\key{trdlmd}, \textbf{key\_diatrd...})]
                   {Tracer/Dynamics Trends (\key{trdlmd}, \key{diatrdtra}, \key{diatrddyn})}
+\subsection[Tracer/Dynamics Trends (TRD)]
+                  {Tracer/Dynamics Trends (\key{trdmld}, \key{trdtra}, \key{trddyn}, \key{trdmld\_trc})}
 \label{MISC_tratrd}
+%to be udated this corresponds to OPA8
+When \key{diatrddyn} and/or \key{diatrddyn} cpp variables are defined, each
+%------------------------------------------namtrd----------------------------------------------------
+\namdisplay{namtrd}
+%-------------------------------------------------------------------------------------------------------------
+When \key{trddyn} and/or \key{trddyn} CPP variables are defined, each
 trend of the dynamics and/or temperature and salinity time evolution equations
 is stored in three-dimensional arrays just after their computation ($i.e.$ at the end
+of each $dyn\cdots .F90$ and/or $tra\cdots .F90$ routine). These trends are then
+used in diagnostic routines $diadyn.F90$ and $diatra.F90$ respectively.
+In the standard model, these routines check the basin averaged properties of
+the momentum and tracer equations every \textit{ntrd } time-steps (\textbf{namelist
+parameter}). These routines are supplied as an example; they must be adapted by
+the user to his/her requirements.
+These two options imply the creation of several extra arrays in the in-core
+memory, increasing quite seriously the code memory requirements.
+of each $dyn\cdots.F90$ and/or $tra\cdots.F90$ routines). These trends are then
+used in \mdl{trdmod} (see TRD directory) every \textit{nn\_trd } time-steps.
+What is done depends on the CPP keys defined:
+\begin{description}
+\item[\key{trddyn}, \key{trdtra}] : a check of the basin averaged properties of the momentum
+and/or tracer equations is performed ;
+\item[\key{trdvor}] : a vertical summation of the moment tendencies is performed,
+then the curl is computed to obtain the barotropic vorticity tendencies which are output ;
+\item[\key{trdmld}] : output of the tracer tendencies averaged vertically
+either over the mixed layer (\np{nn\_ctls}=0),
+or       over a fixed number of model levels (\np{nn\_ctls}$>$1 provides the number of level),
+or       over a spatially varying but temporally fixed number of levels (typically the base
+of the winter mixed layer) read in \ifile{ctlsurf\_idx} (\np{nn\_ctls}=1).
+\end{description}
+The units in the output file can be changed using the \np{nn\_ucf} namelist parameter.
+For example, in case of salinity tendency the units are given by PSU/s/\np{nn\_ucf}.
+Setting \np{nn\_ucf}=86400 provides the tendencies in PSU/d.
+When \key{trdmld} is defined, two time averaging procedure are proposed.
+Setting \np{ln\_trdmld\_instant} to \textit{true}, a simple time averaging is performed,
+so that the resulting tendency is the contribution to the change of a quantity between
+the two instantaneous values taken at the extremities of the time averaging period.
+Setting \np{ln\_trdmld\_instant} to \textit{false}, a double time averaging is performed,
+so that the resulting tendency is the contribution to the change of a quantity between
+two \textit{time mean} values. The later option requires the use of an extra file, \ifile{restart\_mld}
+(\np{ln\_trdmld\_restart}=true), to restart a run.
+Note that the mixed layer tendency diagnostic can also be used on biogeochemical models
+via Êthe \key{trdtrc} and \key{trdmld\_trc} CPP keys.
 % -------------------------------------------------------------------------------------------------------------
 %       On-line Floats trajectories
 % -------------------------------------------------------------------------------------------------------------
 \subsection{On-line Floats trajectories (FLO)}
+\subsection{On-line Floats trajectories (FLO) (\key{floats}}
 \label{FLO}
 %--------------------------------------------namflo-------------------------------------------------------
 …
 %--------------------------------------------------------------------------------------------------------------
 The on-line computation of floats adevected either by the three dimensional velocity
+The on-line computation of floats advected either by the three dimensional velocity
 field or constraint to remain at a given depth ($w = 0$ in the computation) have been
+introduced in the system during the CLIPPER project. The algorithm used is based on
+the work of \cite{Blanke_Raynaud_JPO97}. (see also the web site describing the off-line
+use of this marvellous diagnostic tool (http://stockage.univ-brest.fr/~grima/Ariane/).
+introduced in the system during the CLIPPER project. The algorithm used is based
+either on the work of \cite{Blanke_Raynaud_JPO97} (default option), or on a $4^th$
+Runge-Hutta algorithm (\np{ln\_flork4}=true). Note that the \cite{Blanke_Raynaud_JPO97}
+algorithm have the advantage of providing trajectories which are consistent with the
+numeric of the code, so that the trajectories never intercept the bathymetry.
+See also the web site describing the off-line use of this marvellous diagnostic tool
+(http://stockage.univ-brest.fr/~grima/Ariane/).
 % -------------------------------------------------------------------------------------------------------------
 %       Other Diagnostics
 % -------------------------------------------------------------------------------------------------------------
 \subsection{Other Diagnostics}
+\subsection{Other Diagnostics (\key{diahth}, \key{diaar5})}
 \label{MISC_diag_others}
-%To be updated  this mainly corresponds to OPA 8
 Aside from the standard model variables, other diagnostics can be computed
+on-line or can be added to the model. The available ready-to-add diagnostics
+routines can be found in directory DIA. Among the available diagnostics are:
+- the mixed layer depth (based on a density criterion) (\mdl{diamxl})
+- the turbocline depth (based on a turbulent mixing coefficient criterion) (\mdl{diamxl})
+- the depth of the 20\r{}C isotherm (\mdl{diahth})
+on-line. The available ready-to-add diagnostics routines can be found in directory DIA.
+Among the available diagnostics the following ones are obtained when defining
+the \key{diahth} CPP key:
+- the mixed layer depth (based on a density criterion, \citet{de_Boyer_Montegut_al_JGR04}) (\mdl{diahth})
+- the turbocline depth (based on a turbulent mixing coefficient criterion) (\mdl{diahth})
+- the depth of the 20\deg C isotherm (\mdl{diahth})
 - the depth of the thermocline (maximum of the vertical temperature gradient) (\mdl{diahth})
+- the meridional heat and salt transports and their decomposition (\mdl{diamfl})
+The poleward heat and salt transports, their advective and diffusive component, and
+the meriodional stream function can be computed on-line in \mdl{diaptr} by setting
+\np{ln\_diaptr} to true (see the \textit{namptr} namelist below).
+When \np{ln\_subbas}~=~true, transports and stream function are computed
+for the Atlantic, Indian, Pacific and Indo-Pacific Oceans (defined north of 30\deg S)
+as well as for the World Ocean. The sub-basin decomposition requires an input file
+(\ifile{subbasins}) which contains three 2D mask arrays, the Indo-Pacific mask
+been deduced from the sum of the Indian and Pacific mask (Fig~\ref{Fig_mask_subasins}).
+%------------------------------------------namptr----------------------------------------------------
+\namdisplay{namptr}
+%-------------------------------------------------------------------------------------------------------------
+%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+\begin{figure}[!t] \label{Fig_mask_subasins}  \begin{center}
+\includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_mask_subasins.pdf}
+\caption {Decomposition of the World Ocean (here ORCA2) into sub-basin used in to compute
+the heat and salt transports as well as the meridional stream-function: Atlantic basin (red),
+Pacific basin (green), Indian basin (bleue), Indo-Pacific basin (bleue+green).
+Note that semi-enclosed seas (Red, Med and Baltic seas) as well as Hudson Bay
+are removed from the sub-basin. Note also that the Arctic Ocean has been split
+into Atlantic and Pacific basins along the North fold line.  }
+\end{center}   \end{figure}
+%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 In addition, a series of diagnostics has been added in the \mdl{diaar5}.
 …
 the \key{diaar5} defined to be called.
+% ================================================================
+% predefined configurations
+% ================================================================
+\section{predefined configurations}
+\label{MISC_config}
+There is several predefined ocean configuration which use is controlled by a specific CPP key.
+The key set the domain sizes (\jp{jpiglo}, \jp{jpjglo}, \jp{jpk}), the mesh and the bathymetry,
+and, in some cases, add to the model physics some specific treatments.
+% -------------------------------------------------------------------------------------------------------------
+%       ORCA family configurations
+% -------------------------------------------------------------------------------------------------------------
+\subsection{ORCA family: global ocean with tripolar grid}
+\label{MISC_config_orca}
+The NEMO system is provided with four built-in ORCA configurations which differ in the
+horizontal resolution used:
+\begin{description}
+\item[\key{orca\_r4}]  \jp{cp\_cfg}~=~orca ; \jp{jp\_cfg}~=~4
+\item[\key{orca\_r2}]  \jp{cp\_cfg}~=~orca ; \jp{jp\_cfg}~=~2
+\item[\key{orca\_r1}]  \jp{cp\_cfg}~=~orca ; \jp{jp\_cfg}~=~1
+\item[\key{orca\_r05}]  \jp{cp\_cfg}~=~orca ; \jp{jp\_cfg}~=~05
+\item[\key{orca\_r025}]  \jp{cp\_cfg}~=~orca ; \jp{jp\_cfg}~=~025
+\end{description}
+\subsubsection{ORCA mesh}
+%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+\begin{figure}[!t] \label{Fig_MISC_ORCA_msh}  \begin{center}
+\includegraphics[width=0.98\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_mesh.pdf}
+\caption {ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\deg N.
+The two "north pole" are the foci of a series of embedded ellipses (blue curves)
+which are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes).
+Then, following \citet{Madec_Imbard_CD96}, the normal to the series of ellipses (red curves) is computed
+which provide the j-lines of the mesh (pseudo longitudes).
+ }
+\end{center}   \end{figure}
+%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+\begin{figure}[!tbp] \label{Fig_MISC_ORCA_e1e2}  \begin{center}
+\includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_msh05_e1_e2.pdf}
+\includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_ORCA_aniso.pdf}
+\caption {\textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and
+\textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
+for ORCA 0.5\deg ~mesh. South of 20\deg N a Mercator grid is used ($e_1 = e_2$)
+so that the anisotropy ratio is 1. Poleward of 20\deg N, the two "north pole"
+introduce a weak anisotropy over the ocean areas ($< 1.2$) except in vicinity of Victoria Island
+(Canadian Arctic Archipelago). }
+\end{center}   \end{figure}
+%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+%--------------------------------------------------TABLE--------------------------------------------------
+\begin{table}[htbp]  \label{Tab_ORCA}
+\begin{center}
+\begin{tabular}{ccccc}
+key                         & \jp{jp\_cfg} &  \jp{jpiglo} & \jp{jpiglo} &       \\
+\hline  \hline
+\key{orca\_r4}        &        4         &         92     &      76      &       \\
+\key{orca\_r2}       &        2         &       182     &    149      &        \\
+%\key{orca\_r1}       &        1         &       362     &     511     &        \\
+\key{orca\_r05}     &        05       &       722     &     261     &        \\
+\key{orca\_r025}   &        025     &      1442    &   1021     &        \\
+%\key{orca\_r8}       &        8         &      2882    &   2042     &        \\
+%\key{orca\_r12}     &      12         &      4322    &   3062      &       \\
+\hline
+\hline
+\end{tabular}
+\caption {Set of predefined ORCA parameters. }
+\end{center}
+\end{table}
+%--------------------------------------------------------------------------------------------------------------
+The tripolar grid used in ORCA configuration ....
+NB: the two north poles position has been chosen to minimise the anisotropy ratio in
+the Gulf Stream and kuroshio areas, two highly turbulent regions.
+ORCA~2 : a $2\deg$ zonal resolution, and a meridional resolution varying from $0.5\deg$ at the
+equator to $2\deg cos\phi$ south of $20\deg$S (Fig. 1). The grid features two points of convergence in the
+Northern Hemisphere, both situated on continents. Minimum resolution in high latitudes is about
+~km in the Arctic and 50~km in the Antarctic. Local mesh refinements are applied to the
+Mediterranean, Red, Black and Caspian Seas. None of them appears to be of particular
+importance for the study of high latitude climate, but the fine resolution is needed in order to have
+their local circulation and their role in the World Ocean's circulation considered correctly.
+ORCA2-LIM (global ocean sea-ice configuration \citep{Timmermann_al_OM05}.
+The horizontal mesh is based on a $2\deg \times 2\deg$ Mercator grid ($i.e.$ same zonal and
+meridional grid spacing) which has been modified poleward
+of $20\deg$N in order to include two numerical inland poles \citep{Murray_JCP96}.
+This modification is semi-analytical \citep{Madec_Imbard_CD96}
+and based on a series of embedded ellipses. It insures that the mesh remains
+close to isotropy and that the smallest grid cell is along Antarctica.
+In order to refine the meridional resolution up to $0.5\deg$ at the equator,
+additional local transformations were applied with in the Tropics.
+Local mesh refinements are also applied to the Mediterranean, Red, Black
+and Caspian Seas so that the resolution is $1\deg \time 1\deg$ there.
+There are 31 levels in the vertical, with the highest resolution (10m)
+in the upper 150m. The bottom topography and the coastlines are derived
+from the global atlas of Smith and Sandwell (1997).
+\key{orca\_lev10} 10 time more vertical levels
+\key{agrif}  : ORCA2-LIM plus an AGRIF zoom over the Agulhas current area
+\key{arctic}, \key{antarctic}  (not used in ORCA\_R4)
+We thus only provide a brief introduction in this chapter.
+The global coupled ocean-ice configuration is very similar to that used as part of the climate
+model developed at GFDL for the 4th IPCC assessment of climate change (Griffies et al., 2005;
+Gnanadesikan et al., 2006).
+The ORCA2-LIM configuration is also the basis for the \NEMO contribution to the
+Coordinate Ocean-ice Reference Experiments (COREs) documented in \citet{Griffies_al_OM09}.
+These experiments employ the boundary forcing from \citet{Large_Yeager_Rep04} (see \S\ref{SBC_blk_core}),
+which was developed for the purpose of running global coupled ocean-ice simulations without an
+interactive atmosphere. This \citet{Large_Yeager_Rep04} dataset is available through the GFDL web
+site \footnote{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}.
+The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the \NEMO distribution
+since release v3.3.
+% -------------------------------------------------------------------------------------------------------------
+%       GYRE family configuration
+% -------------------------------------------------------------------------------------------------------------
+\subsection{GYRE family: double gyre basin (\key{gyre})}
+\label{MISC_config_gyre}
+The GYRE configuration \citep{Levy_al_OM10} have been built to simulated
+the seasonal cycle of a double-gyre box model. It consist in an idealized domain
+similar to that used in the studies of \citet{Drijfhout_JPO94} and \citet{Hazeleger_Drijfhout_JPO98,
+Hazeleger_Drijfhout_JPO99, Hazeleger_Drijfhout_JGR00, Hazeleger_Drijfhout_JPO00},
+over which an analytical seasonal forcing is applied. This allows to investigate the
+spontaneous generation of a large number of interacting, transient mesoscale eddies
+and their contribution to the large scale circulation.
+The domain geometry is a closed rectangular basin on the $\beta$-plane centred
+at $\sim 30\deg$N and rotated by 45\deg, 3180~km long, 2120~km wide
+and 4~km deep (Fig.~\ref{Fig_MISC_strait_hand}).
+The domain is bounded by vertical walls and by a ßat bottom. The configuration is
+meant to represent an idealized North Atlantic or North Pacific basin.
+The circulation is forced by analytical profiles of wind and buoyancy ßuxes.
+The applied forcings vary seasonally in a sinusoidal manner between winter
+and summer extrema \citep{Levy_al_OM10}.
+The wind stress is zonal and its curl changes sign at 22\deg N and 36\deg N.
+It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain
+and a small recirculation gyre in the southern corner.
+The net heat ßux takes the form of a restoring toward a zonal apparent air
+temperature profile. A portion of the net heat ßux which comes from the solar radiation
+is allowed to penetrate within the water column.
+The fresh water ßux is also prescribed and varies zonally.
+It is determined such as, at each time step, the basin-integrated ßux is zero.
+The basin is initialised at rest with vertical profiles of temperature and salinity
+uniformly applied to the whole domain.
+The GYRE configuration is set through the \key{gyre} CPP key. Its horizontal resolution
+(and thus the size of the domain) is determined by setting \jp{jp\_cfg} in \hf{par\_GYRE} file: \\
+\jp{jpiglo} $= 30 \times$ \jp{jp\_cfg} + 2   \\
+\jp{jpjglo} $= 20 \times$ \jp{jp\_cfg} + 2   \\
+Obviously, the namelist parameters have to be adjusted to the chosen resolution.
+In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}=31) (Fig.~\ref{Fig_zgr}).
+The GYRE configuration is also used in benchmark test as it is very simple to increase
+its resolution and as it does not requires any input file. For example, keeping a same model size
+on each processor while increasing the number of processor used is very easy, even though the
+physical integrity of the solution can be compromised.
+%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+\begin{figure}[!t] \label{Fig_GYRE}  \begin{center}
+\includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_GYRE.pdf}
+\caption {Snapshot of relative vorticity at the surface of the model domain
+in GYRE R9, R27 and R54. From \citet{Levy_al_OM10}.}
+\end{center}   \end{figure}
+%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+% -------------------------------------------------------------------------------------------------------------
+%       EEL family configuration
+% -------------------------------------------------------------------------------------------------------------
+\subsection{EEL family: periodic channel}
+\label{MISC_config_EEL}
+\begin{description}
+\item[\key{eel\_r2}]
+\item[\key{eel\_r5}]
+\item[\key{eel\_r6}]
+\end{description}
+% -------------------------------------------------------------------------------------------------------------
+%       POMME configuration
+% -------------------------------------------------------------------------------------------------------------
+\subsection{POMME: mid-latitude sub-domain}
+\label{MISC_config_POMME}
+\key{pomme\_r025}

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_Model_Basics.tex

-                      r2282
+                      r2349
 \label{PE_zco_tilde}
+The $\tilde{z}$-coordinate has been developed by \citet{Leclair_Madec_OM10s}.
+It is not available in the current version of \NEMO.
 \newpage

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_OBS.tex

-                      r2298
+                      r2349
 The OBS branch is a diagnostic branch which reads in observation files (profile temperature and
 salinity, sea surface temperature, sea level anomaly and sea ice concentration) and calculates the
+salinity, sea surface temperature, sea level anomaly and sea ice concentration) and calculates
 an interpolated model equivalent value at the observation location and nearest model timestep.
 This is code with was originally developed for use with NEMOVAR.
 …
 The resulting data is saved in a ``feedback'' file or files which can be used for model validation
 and verification and also to provide information for data assimilation. This code is controlled by
 the namelist \np{nam\_obs}. To build with the OBS code active \np{key\_diaobs} must be set.
+the namelist \textit{nam\_obs}. To build with the OBS code active \key{diaobs} must be set.
 There is a brief description of all the namelist options provided.
+Missing information: description of \key{sp}, \key{datetime\_out}
 …
 run and build of NEMO to run the observation operator.
 First compile NEMO with \np{key\_diaobs} set.
+First compile NEMO with \key{diaobs} set.
 Next download some ENSEMBLES EN3 data from the website http://www.hadobs.org.
 …
 You will need to add the following to the namelist to run the observation
 operator on this data - replace \np{profiles\_01.nc} with the observation file you
 wish to use (or link in):
+operator on this data - set the \np{enactfiles} namelist parameter to the observation
+file name you wish to use (or link in):
 %------------------------------------------namobs_example-----------------------------------------------------

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_SBC.tex

-                      r2282
+                      r2349
  ================================================================
+% ================================================================
 % Chapter Ñ Surface Boundary Condition (SBC)
 % ================================================================
 …
 The ocean needs six fields as surface boundary condition:
 \begin{itemize}
 \item the two components of the surface ocean stress $\left( {\tau _u \;,\;\tau _v} \right)$
 \item the incoming solar and non solar heat fluxes $\left( {Q_{ns} \;,\;Q_{sr} } \right)$
 \item the surface freshwater budget $\left( {\textit{emp},\;\textit{emp}_S } \right)$
+   \item the two components of the surface ocean stress $\left( {\tau _u \;,\;\tau _v} \right)$
+   \item the incoming solar and non solar heat fluxes $\left( {Q_{ns} \;,\;Q_{sr} } \right)$
+   \item the surface freshwater budget $\left( {\textit{emp},\;\textit{emp}_S } \right)$
 \end{itemize}
+Four different ways to provide those six fields to the ocean are available which
+are controlled by namelist variables: an analytical formulation (\np{ln\_ana}=true),
+a flux formulation (\np{ln\_flx}=true), a bulk formulae formulation (CORE
+(\np{ln\_core}=true) or CLIO (\np{ln\_clio}=true) bulk formulae) and a coupled
+plus an optional field:
+\begin{itemize}
+   \item the atmospheric pressure at the ocean surface $\left( p_a \right)$
+\end{itemize}
+Four different ways to provide the first six fields to the ocean are available which
+are controlled by namelist variables: an analytical formulation (\np{ln\_ana}~=~true),
+a flux formulation (\np{ln\_flx}~=~true), a bulk formulae formulation (CORE
+(\np{ln\_core}~=~true) or CLIO (\np{ln\_clio}~=~true) bulk formulae) and a coupled
 formulation (exchanges with a atmospheric model via the OASIS coupler)
+(\np{ln\_cpl}=true). The frequency at which the six fields have to be updated is
+the  \np{nf\_sbc} namelist parameter.
+(\np{ln\_cpl}~=~true). The optional atmospheric pressure can be used either
+to force ocean and ice dynamics (\np{ln\_apr\_dyn}~=~true), or in the bulk
+formulae computation (\np{ln\_apr\_dyn}~=~true)
+\footnote{None of the two current bulk formulea (CLIO and CORE) uses the
+atmospheric pressure field.}.
+The frequency at which the six or seven fields have to be updated is 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
 …
 These options control  the rotation of vector components supplied relative to an east-north
 coordinate system onto the local grid directions in the model; the addition of a surface
 restoring term to observed SST and/or SSS (\np{ln\_ssr}=true); the modification of fluxes
+restoring term to observed SST and/or SSS (\np{ln\_ssr}~=~true); the modification of fluxes
 below ice-covered areas (using observed ice-cover or a sea-ice model)
 (\np{nn\_ice}=0,1, 2 or 3); the addition of river runoffs as surface freshwater
 fluxes (\np{ln\_rnf}=true); the addition of a freshwater flux adjustment in
 order to avoid a mean sea-level drift (\np{nn\_fwb}= 0, 1 or 2); and the
+(\np{nn\_ice}~=~0,1, 2 or 3); the addition of river runoffs as surface freshwater
+fluxes or lateral inflow (\np{ln\_rnf}~=~true); the addition of a freshwater flux adjustment
+in order to avoid a mean sea-level drift (\np{nn\_fwb}~=~0,~1~or~2); and the
 transformation of the solar radiation (if provided as daily mean) into a diurnal
 cycle (\np{ln\_dm2dc}=true).
+cycle (\np{ln\_dm2dc}~=~true).
 In this chapter, we first discuss where the surface boundary condition appears in the
 …
 %created!)
+%
 %Especially the \np{nf\_sbc}, the \mdl{sbc\_oce} module (fluxes + mean sst sss ssu
+%Especially the \np{nn\_fsbc}, the \mdl{sbc\_oce} module (fluxes + mean sst sss ssu
 %ssv) i.e. information required by flux computation or sea-ice
+%
 …
 %--------------------------------------------------------------------------------------------------------------
 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
 …
 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 GFDL web
+site (http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html).
 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}.
 The required 8 input fields are:
 …
 In the coupled formulation of the surface boundary condition, the fluxes are
+provided by the OASIS coupler at each \np{nf\_cpl} time-step, while sea and ice
+surface temperature, ocean and ice albedo, and ocean currents are sent to
+the atmospheric component.
+The generalised coupled interface is under development. It should be available
+in summer 2008. It will include the ocean interface for most of the European
+atmospheric GCM (ARPEGE, ECHAM, ECMWF, HadAM, LMDz).
+provided by the OASIS coupler at a frequency which is defined in the OASIS coupler,
+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
+(\key{oasis3}) and does not support OASIS 4
+\footnote{The \key{oasis4} exist. It activates portion of the code that are still under development.}.
+It has been successfully used to interface \NEMO to most of the European atmospheric
+GCM (ARPEGE, ECHAM, ECMWF, HadAM, LMDz),
+as well as to WRF (Weather Research and Forecasting Model) (http://wrf-model.org/).
+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 recieved 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}. In this case,
+CO$_2$ fluxes are exchanged between the atmosphere and the ice-ocean system.
+% ================================================================
+%        Atmospheric pressure
+% ================================================================
+\section   [Atmospheric pressure (\textit{sbcapr})]
+         {Atmospheric pressure (\mdl{sbcapr})}
+\label{SBC_apr}
+%------------------------------------------namsbc_apr----------------------------------------------------
+\namdisplay{namsbc_apr}
+%-------------------------------------------------------------------------------------------------------------
+The optional atmospheric pressure can be used either to force ocean and ice dynamics
+(\np{ln\_apr\_dyn}~=~true), or in the bulk formulae computation (\np{ln\_apr\_dyn}~=~true).
+The input atmospheric forcing is interpolated in time to the model time step, and optionally
+in space when interpolation on-the-fly is used. When used to force the dynamics, it is further
+transformed into an equivalent inverse barometer sea surface height, $\eta_{ib}$, using:
+\begin{equation} \label{SBC_ssh_ib}
+   \eta_{ib} = -  \frac{1}{g\,\rho_o}  \left( P_{atm} - P_o \right)
+\end{equation}
+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, $i.e.$ the mean value of
+$\eta_{ib}$ is kept to zero at all time step.
+A 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).
+Furthermore, $\eta_{ib}$ can be set in the output. This simplifies the altirmetry data
+and model comparison as inverse barometer sea surface height is usually removed
+from thise date prior to their distribution.
 % ================================================================
 %        River runoffs
 % ================================================================
 \section   [river runoffs (\textit{sbcrnf})]
          {river runoffs (\mdl{sbcrnf})}
+\section   [River runoffs (\textit{sbcrnf})]
+         {River runoffs (\mdl{sbcrnf})}
 \label{SBC_rnf}
 %------------------------------------------namsbc_rnf----------------------------------------------------
 …
 required to properly represent the diurnal cycle \citep{Bernie_al_JC05}. see also \S\ref{SBC_dcy}.}.
 As such from VN3.3 onwards it is possible to add river runoff through a non-zero depth, and for the
+As such from V~3.3 onwards it is possible to add river runoff through a non-zero depth, and for the
 temperature and salinity of the river to effect the surrounding ocean.
 The user is able to specify, in a NetCDF input file, the temperature and salinity of the river, along with the
 …
 After the user specified depth is read ini, the number of grid boxes this corresponds to is
 calculated and stored in the variable \np{nz\_rnf}.
 The variable \np{h\_dep} is then calculated to be the depth (in metres) of the bottom of the
+The variable \textit{h\_dep} is then calculated to be the depth (in metres) of the bottom of the
 lowest box the river water is being added to (i.e. the total depth that river water is being added to in the model).
 The mass/volume addition due to the river runoff is, at each relevant depth level, added to the horizontal divergence (\np{hdivn})
 in the subroutine \np{sbc\_rnf\_div} (called from \np{divcur}).
+The mass/volume addition due to the river runoff is, at each relevant depth level, added to the horizontal divergence
+(\textit{hdivn}) in the subroutine \rou{sbc\_rnf\_div} (called from \mdl{divcur}).
 This increases the diffusion term in the vicinity of the river, thereby simulating a momentum flux.
 The sea surface height is calculated using the sum of the horizontal divergence terms, and so the
 river runoff indirectly forces an increase in sea surface height.
 The \np{hdivn} terms are used in the tracer advection modules to force vertical velocities.
+The \textit{hdivn} terms are used in the tracer advection modules to force vertical velocities.
 This causes a mass of water, equal to the amount of runoff, to be moved into the box above.
 The heat and salt content of the river runoff is not included in this step, and so the tracer
 …
 As such the volume of water does not change, but the water is diluted.
 For the non-linear free surface case (vvl), no flux is allowed through the surface.
+For the non-linear free surface case (\key{vvl}), 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.
 …
 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 setting \np{ln\_dm2dc}=true (a \textit{namsbc} namelist parameter) when using
 CORE bulk formulea (\np{ln\_blk\_core}=true) or the flux formulation (\np{ln\_flx}=true).
+in \NEMO by setting \np{ln\_dm2dc}~=~true (a \textit{namsbc} namelist parameter) when using
+CORE bulk formulea (\np{ln\_blk\_core}~=~true) or the flux formulation (\np{ln\_flx}~=~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
 …
 %-------------------------------------------------------------------------------------------------------------
 In forced mode using a flux formulation (default option or \key{flx} defined), a
+In forced mode using a flux formulation (\np{ln\_flx}~=~true), a
 feedback term \emph{must} be added to the surface heat flux $Q_{ns}^o$:
 \begin{equation} \label{Eq_sbc_dmp_q}

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_TRA.tex

-                      r2286
+                      r2349
 %        Bottom Boundary Condition
 % -------------------------------------------------------------------------------------------------------------
 \subsection   [Bottom Boundary Condition (\textit{trabbc} - \key{bbc})]
          {Bottom Boundary Condition (\mdl{trabbc} - \key{bbc})}
+\subsection   [Bottom Boundary Condition (\textit{trabbc})]
+         {Bottom Boundary Condition (\mdl{trabbc})}
 \label{TRA_bbc}
 %--------------------------------------------nambbc--------------------------------------------------------
 …
 Bottom Water) by a few Sverdrups  \citep{Emile-Geay_Madec_OS09}.
+The presence of geothermal heating is controlled by the namelist
+parameter  \np{nn\_geoflx}. When this parameter is set to 1, a constant
+geothermal heating is introduced whose value is given by the
+\np{nn\_geoflx\_cst}, which is also a namelist parameter. When it is set to 2,
+a spatially varying geothermal heat flux is introduced which is provided
+in the \ifile{geothermal\_heating} NetCDF file (Fig.\ref{Fig_geothermal}).
+The presence of geothermal heating is controlled by setting the namelist
+parameter  \np{ln\_trabbc} to true. Then, when \np{nn\_geoflx} is set to 1,
+a constant geothermal heating is introduced whose value is given by the
+\np{nn\_geoflx\_cst}, which is also a namelist parameter.
+When  \np{nn\_geoflx} is set to 2, a spatially varying geothermal heat flux is
+introduced which is provided in the \ifile{geothermal\_heating} NetCDF file
+(Fig.\ref{Fig_geothermal}) \citep{Emile-Geay_Madec_OS09}.
 % ================================================================

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_ZDF.tex

-                      r2282
+                      r2349
 \label{ZDF_gls}
 %--------------------------------------------namgls---------------------------------------------------------
 \namdisplay{namgls}
+%--------------------------------------------namzdf_gls---------------------------------------------------------
+\namdisplay{namzdf_gls}
 %--------------------------------------------------------------------------------------------------------------
 …
 The constants $C_1$, $C_2$, $C_3$, ${\sigma_e}$, ${\sigma_{\psi}}$ and the wall function ($Fw$)
 depends of the choice of the turbulence model. Four different turbulent models are pre-defined
 (Tab.\ref{Tab_GLS}). They are made available through th \np{gls} namelist parameter.
+(Tab.\ref{Tab_GLS}). They are made available through the \np{nn\_clo} namelist parameter.
 %--------------------------------------------------TABLE--------------------------------------------------
 …
 \hline
 \end{tabular}
 \caption {Set of predefined GLS parameters, or equivalently predefined turbulence models available with \key{gls} and controlled by the \np{nn\_clos} namelist parameter.}
+\caption {Set of predefined GLS parameters, or equivalently predefined turbulence models available with \key{zdfgls} and controlled by the \np{nn\_clos} namelist parameter.}
 \end{center}
 \end{table}
 …
 In the Mellor-Yamada model, the negativity of $n$ allows to use a wall function to force
 the convergence of the mixing length towards $K\,z_b$ ($K$: Kappa and $z_b$: rugosity length)
+the convergence of the mixing length towards $K z_b$ ($K$: Kappa and $z_b$: rugosity length)
 value near physical boundaries (logarithmic boundary layer law). $C_{\mu}$ and $C_{\mu'}$
 are calculated from stability function proposed by \citet{Galperin_al_JAS88}, or by \citet{Kantha_Clayson_1994}
 …
 stably stratified situations, and that its value has to be chosen in accordance
 with the algebraic model for the turbulent ßuxes. The clipping is only activated
 if \np{ln\_length\_lim}=true, and the $c_{lim}$ is set to the \np{clim\_galp} value.
+if \np{ln\_length\_lim}=true, and the $c_{lim}$ is set to the \np{rn\_clim\_galp} value.
 % -------------------------------------------------------------------------------------------------------------
 …
 %       Turbulent Closure Scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsection{Turbulent Closure Scheme (\key{zdftke})}
+\subsection{Turbulent Closure Scheme (\key{zdftke} or \key{zdfgls})}
 \label{ZDF_tcs}
 The TKE turbulent closure scheme presented in \S\ref{ZDF_tke} and used
 when the \key{zdftke} is defined, in theory solves the problem of statically
+The turbulent closure scheme presented in \S\ref{ZDF_tke} and \S\ref{ZDF_gls}
+(\key{zdftke} or \key{zdftke} is defined) in theory solves the problem of statically
 unstable density profiles. In such a case, the term corresponding to the
 destruction of turbulent kinetic energy through stratification in \eqref{Eq_zdftke_e}
 becomes a source term, since $N^2$ is negative. It results in large values of
 $A_T^{vT}$ and  $A_T^{vT}$, and also the four neighbouring
+or \eqref{Eq_zdfgls_e} becomes a source term, since $N^2$ is negative.
+It results in large values of $A_T^{vT}$ and  $A_T^{vT}$, and also the four neighbouring
 $A_u^{vm} {and}\;A_v^{vm}$ (up to $1\;m^2s^{-1})$. These large values
 restore the static stability of the water column in a way similar to that of the
 …
 in the vicinity of the sea surface (first ocean layer), the eddy coefficients
 computed by the turbulent closure scheme do not usually exceed $10^{-2}m.s^{-1}$,
 because the mixing length scale is bounded by the distance to the sea surface
 (see \S\ref{ZDF_tke}). It can thus be useful to combine the enhanced vertical
+because the mixing length scale is bounded by the distance to the sea surface.
+It can thus be useful to combine the enhanced vertical
 diffusion with the turbulent closure scheme, $i.e.$ setting the \np{ln\_zdfnpc}
 namelist parameter to true and defining the \key{zdftke} CPP key all together.
+namelist parameter to true and defining the turbulent closure CPP key all together.
 The KPP turbulent closure scheme already includes enhanced vertical diffusion
 …
 % Double Diffusion Mixing
 % ================================================================
 \section  [Double Diffusion Mixing (\textit{zdfddm} - \key{zdfddm})]
       {Double Diffusion Mixing (\mdl{zdfddm} module - \key{zdfddm})}
+\section  [Double Diffusion Mixing (\key{zdfddm})]
+      {Double Diffusion Mixing (\key{zdfddm})}
 \label{ZDF_ddm}
 …
 parameterisation of such phenomena in a global ocean model and show that
 it leads to relatively minor changes in circulation but exerts significant regional
+influences on temperature and salinity.
+influences on temperature and salinity. This parameterisation has been
+introduced in \mdl{zdfddm} module and is controlled by the \key{zdfddm} CPP key.
 Diapycnal mixing of S and T are described by diapycnal diffusion coefficients
 …
 \end{align*}
 where subscript $f$ represents mixing by salt fingering, $d$ by diffusive convection,
+and $o$ by processes other than double diffusion. The rates of double-diffusive mixing depend on the buoyancy ratio $R_\rho = \alpha \partial_z T / \beta \partial_z S$,
+and $o$ by processes other than double diffusion. The rates of double-diffusive
+mixing depend on the buoyancy ratio $R_\rho = \alpha \partial_z T / \beta \partial_z S$,
 where $\alpha$ and $\beta$ are coefficients of thermal expansion and saline
 contraction (see \S\ref{TRA_eos}). To represent mixing of $S$ and $T$ by salt
 …
 % Tidal Mixing
 % ================================================================
 \section{Tidal Mixing}
+\section{Tidal Mixing (\key{zdftmx})}
 \label{ZDF_tmx}
 …
 %        Indonesian area specific treatment
 % -------------------------------------------------------------------------------------------------------------
 \subsection{Indonesian area specific treatment}
+\subsection{Indonesian area specific treatment (\np{ln\_zdftmx\_itf})}
 \label{ZDF_tmx_itf}

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Introduction.tex

-                      r2282
+                      r2349
 are used throughout.
+The following chapters deal with the discrete equations. Chapter~\ref{DOM} presents the
+space and time domain. The model is discretised on a staggered grid (Arakawa C grid)
+with masking of land areas and uses a Leap-frog environment for time-stepping. Vertical
+discretisation used depends on both how the bottom topography is represented and
+The following chapters deal with the discrete equations. Chapter~\ref{STP} presents the
+time domain. The model time stepping environment is a three level scheme in which
+the tendency terms of the equations are evaluated either centered  in time, or forward,
+or backward depending of the nature of the term.
+Chapter~\ref{DOM} presents the space domain. The model is discretised on a staggered grid
+(Arakawa C grid) with masking of land areas and uses a Leap-frog environment for time-stepping.
+Vertical discretisation used depends on both how the bottom topography is represented and
 whether the free surface is linear or not. Full step or partial step $z$-coordinate or
 $s$- (terrain-following) coordinate is used with linear free surface (level position are then
 …
 function of the sea surface heigh). The following two chapters (\ref{TRA} and \ref{DYN})
 describe the discretisation of the prognostic equations for the active tracers and the
 momentum. Explicit, split-explicit and implicit free surface formulations are implemented
 as well as rigid-lid case. A number of numerical schemes are available for momentum
 advection, for the computation of the pressure gradients, as well as for the advection of
 tracers (second or higher order advection schemes, including positive ones).
+momentum. Explicit, split-explicit and filtered free surface formulations are implemented.
+A number of numerical schemes are available for momentum advection, for the computation
+of the pressure gradients, as well as for the advection of tracers (second or higher
+order advection schemes, including positive ones).
 Surface boundary conditions (chapter~\ref{SBC}) can be implemented as prescribed
 …
 with a sea ice model (LIM) and with biogeochemistry models (PISCES, LOBSTER).
 Interactive coupling to Atmospheric models is possible via the OASIS coupler
+\citep{OASIS2006}.
+\citep{OASIS2006}. Two-way nesting is also available through an interface to the
+AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}.
 Other model characteristics are the lateral boundary conditions (chapter~\ref{LBC}).
 …
 space and time variable coefficient \citet{Treguier1997}. The model has vertical harmonic
 viscosity and diffusion with a space and time variable coefficient, with options to compute
 the coefficients with \citet{Blanke1993}, \citet{Large_al_RG94}, or \citet{Pacanowski_Philander_JPO81} mixing
 schemes.
+the coefficients with \citet{Blanke1993}, \citet{Large_al_RG94}, \citet{Pacanowski_Philander_JPO81},
+or \citet{Umlauf_Burchard_JMS03} mixing schemes.
+Specific online diagnostics (not documented yet) are available in the model: output of all
+Chapter~\ref{OBS} describes a tool which reads in observation files (profile temperature and salinity,
+sea surface temperature, sea level anomaly and sea ice concentration) and calculates an interpolated
+model equivalent value at the observation location and nearest model timestep. Originally
+developed of data assimilation, it is a fantastic tool for model and data comparison.
+Other Specific online diagnostics (not documented yet) are available in the model: output of all
 the tendencies of the momentum and tracers equations, output of tracers tendencies
+averaged over the time evolving mixed layer.
+averaged over the time evolving mixed layer, output of the tendencies of the barotropic
+vorticity equation, on-line floats trajectories...
 The model is implemented in \textsc{Fortran 90}, with preprocessing (C-pre-processor).
 …
 readability of the code it is necessary to follow coding rules. The coding rules for OPA
 include conventions for naming variables, with different starting letters for different types
 of variables (real, integer, parameter\ldots). Those rules are presented in a document
 available on the \NEMO web site.
+of variables (real, integer, parameter\ldots). Those rules are briefly presented in
+Appendix~\ref{Apdx_D} and a more complete document is available on the \NEMO web site.
 The model is organized with a high internal modularity based on physics. For example,
 each trend ($i.e.$, a term in the RHS of the prognostic equation) for momentum and
 tracers is computed in a dedicated module.  To make it easier for the user to find his way
 around the code, the module names follow a three-letter rule. For example, \mdl{tradmp}
 is a module related to the TRAcers equation, computing the DaMPing. The complete list
 of module names is presented in Appendix~\ref{Apdx_D}. Furthermore, modules are
+organized in a few directories that correspond to their category, as indicated by the first
 three letters of their name.
+around the code, the module names follow a three-letter rule. For example, \mdl{traldf}
+is a module related to the TRAcers equation, computing the Lateral DiFfussion.
+The complete list of module names is presented in Appendix~\ref{Apdx_D}.
+Furthermore, modules are organized in a few directories
+ that correspond to their category, as indicated by the first three letters of their name.
 The manual mirrors the organization of the model. After the presentation of the
 continuous equations (Chapter \ref{PE}), the following chapters refer to specific terms of
 the equations each associated with a group of modules .
+The manual mirrors the organization of the model.
+After the presentation of the continuous equations (Chapter \ref{PE}), the following chapters
+refer to specific terms of the equations each associated with a group of modules .
 …
 %\begin{center} \begin{tabular}{|p{143pt}|l|l|} \hline
 \begin{center} \begin{tabular}{|l|l|l|}   \hline
+Chapter \ref{STP} & -                 & model time STePping environment \\    \hline
 Chapter \ref{DOM} & DOM    & model DOMain \\    \hline
 Chapter \ref{TRA} & TRA    & TRAcer equations (potential temperature and salinity) \\   \hline
 Chapter \ref{DYN} & DYN    & DYNamic equations (momentum) \\      \hline
 Chapter \ref{SBC}    & SBC    & Surface Boundary Conditions \\       \hline
 Chapter \ref{LBC} & LBC    & Lateral Boundary Conditions  \\      \hline
+Chapter \ref{LBC} & LBC    & Lateral Boundary Conditions (also OBC and BDY)  \\     \hline
 Chapter \ref{LDF} & LDF    & Lateral DiFfusion (parameterisations) \\   \hline
+Chapter \ref{ZDF} & ZDF    & Vertical DiFfusion  \\      \hline
+Chapter \ref{MISC}   & ...    & Miscellaneous  topics  \\         \hline
+Chapter \ref{ZDF} & ZDF    & vertical (Z) DiFfusion  \\     \hline
+Chapter \ref{OBS} & OBS    & OBServation and model comparison  \\    \hline
+Chapter \ref{ASM} & ASM    & ASsimilation increment  \\     \hline
+Chapter \ref{MISC}   & ...    & Miscellaneous  topics (DIA, DTA, IOM, SOL, TRD, FLO...)    \\         \hline
 \end{tabular}  \end{center}
 \end{table}
-In the current release (v3.0), the LBC directory does not yet exist.
-When created LBC will contain the OBC directory (Open Boundary Condition),
-and the \mdl{lbclnk}, \mdl{mppini} and \mdl{lib\_mpp} modules.
  \vspace{1cm}   Nota Bene : \vspace{0.25cm}
+OPA, like all research tools, is in perpetual evolution. The present document describes
+the OPA version include in the release 3.2 of NEMO. This release differs significantly
+from version 8, documented in \citet{Madec1998}. The main modifications are :\\
+\subsubsection{Changes between releases}
+NEMO/OPA, like all research tools, is in perpetual evolution. The present document describes
+the OPA version include in the release 3.3 of NEMO.  This release differs significantly
+from version 8, documented in \citet{Madec1998}.
+$\bullet$ The main modifications from OPA v8 and NEMO/OPA v3.2 are :\\
 (1) transition to full native \textsc{Fortran} 90, deep code restructuring and drastic
 reduction of CPP keys; \\
 (2) introduction of partial step representation of bottom topography \citep{Barnier_al_OD06}; \\
+(2) introduction of partial step representation of bottom topography \citep{Barnier_al_OD06, Le_Sommer_al_OM09, Penduff_al_OS07}; \\
 (3) partial reactivation of a terrain-following vertical coordinate ($s$- and hybrid $s$-$z$)
 with the addition of several options for pressure gradient computation \footnote{Partial
 …
 new thermodynamics including bulk ice salinity) \citep{Vancoppenolle_al_OM09a, Vancoppenolle_al_OM09b}
+In addition, several minor modifications in the coding have been introduced with the constant concern of improving performance on both scalar and vector computers.
+ \vspace{1cm}
+$\bullet$ The main modifications from NEMO/OPA v3.2 and  v3.2 are :\\
+(1) introduction of a modified leapfrog-Asselin filter time stepping scheme \citep{Leclair_Madec_OM09}; \\
+(2) additional scheme for  iso-neutral mixing \citep{Griffies_al_JPO98}, although it is still a "work in progress"; \\
+(3) a rewriting of the bottom boundary scheme, following \citet{Campin_Goosse_Tel99}; \\
+(4) addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics; \\
+(5) addition of a diurnal cycle on solar radiation \citep{Bernie_al_CD07}; \\
+(6) addition of an on-line observation and model comparison (thanks to NEMOVAR project); \\
+(7) optional application of an assimilation increment (thanks to NEMOVAR project); \\
+(8) introduction of .....
+ \vspace{1cm}
+In addition, several minor modifications in the coding have been introduced with the constant
+concern of improving the model performance.

branches/nemo_v3_3_beta/DOC/TexFiles/Namelist/namasm

-                      r2298
+                      r2349
 !-----------------------------------------------------------------------
+!       nam_asminc    assimilation increments namelist
+&namasm_inc    !   Assimilation increments                               ("key_asminc")
 !-----------------------------------------------------------------------
+! ln_bkgwri   Logical switch for writing out background state
+! ln_trjwri   Logical switch for writing out state trajectory
+! ln_trainc   Logical switch for applying tracer increments
+! ln_dyninc   Logical switch for applying velocity increments
+! ln_sshinc   Logical switch for applying SSH increments
+! ln_asmdin   Logical switch for Direct Initialization (DI)
+! ln_asmiau   Logical switch for Incremental Analysis Updating (IAU)
+! nitbkg      Timestep of background in [0,nitend-nit000-1]
+! nitdin      Timestep of background for DI in [0,nitend-nit000-1]
+! nitiaustr   Timestep of start of IAU interval in [0,nitend-nit000-1]
+! nitiaufin   Timestep of end of IAU interval in [0,nitend-nit000-1]
+! niaufn      Type of IAU weighting function
+! nittrjfrq   Frequency of trajectory output for 4D-VAR
+! ln_salfix   Logical switch for ensuring that the sa > salfixmin
+! salfixmin   Minimum salinity after applying the increments
+&nam_asminc
+    ln_bkgwri = .true.
+    ln_trjwri = .false.
+    ln_trainc = .false.
+    ln_dyninc = .false.
+    ln_sshinc = .false.
+    ln_asmdin = .false.
+    ln_asmiau = .false.
+    nitbkg = 0
+    nitdin = 0
+    nitiaustr = 1
+    nitiaufin = 150
+    niaufn = 0
+    nittrjfrq = 0
+    ln_salfix = .false.
+    salfixmin = -9999
+   ln_bkgwri   = .false.   ! write out background state (T) or not (F)
+   ln_trjwri   = .false.   ! write out state trajectory (T) or not (F)
+   ln_trainc   = .false.   ! apply tracer increments (T) or not (F)
+   ln_dyninc   = .false.   ! apply velocity increments (T) or not (F)
+   ln_sshinc   = .false.   ! applying SSH increments  (T) or not (F)
+   ln_asmdin   = .false.   ! DI: Direct Initialization (T) or not (F)
+   ln_asmiau   = .false.   ! IAU: Incremental Analysis Updating (T) or not (F)
+   nitbkg      =  0        ! timestep of background in [0,nitend-nit000-1]
+   nitdin      =  0        ! timestep of background for DI in [0,nitend-nit000-1]
+   nitiaustr   =  1        ! timestep of start of IAU interval in [0,nitend-nit000-1]
+   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.   ! ensure that the sa > salfixmin (T) or not (F)
+   salfixmin   = -9999     ! Minimum salinity after applying the increments
+/

branches/nemo_v3_3_beta/DOC/TexFiles/Namelist/nambdy

-                      r2282
+                      r2349
 &nambdy        !  unstructured open boundaries                          ("key_bdy")
 !-----------------------------------------------------------------------
+    filbdy_mask    =  ''                  !  name of mask file (if ln_bdy_mask=.TRUE.)
+    filbdy_data_T  = 'bdydata_grid_T.nc'  !  name of data file (T-points)
+    filbdy_data_U  = 'bdydata_grid_U.nc'  !  name of data file (U-points)
+    filbdy_data_V  = 'bdydata_grid_V.nc'  !  name of data file (V-points)
+    filbdy_data_bt_T  = 'bdydata_bt_grid_T.nc'  !  name of data file for Flather condition (T-points)
+    filbdy_data_bt_U  = 'bdydata_bt_grid_U.nc'  !  name of data file for Flather condition (U-points)
+    filbdy_data_bt_V  = 'bdydata_bt_grid_V.nc'  !  name of data file for Flather condition (V-points)
+    ln_bdy_clim    = .false.              !  contain 1 (T) or 12 (F) time dumps and be cyclic
+    ln_bdy_vol     = .true.               !  total volume correction (see volbdy parameter)
+    ln_bdy_mask    = .false.              !  boundary mask from filbdy_mask (T) or boundaries are on edges of domain (F)
+    ln_bdy_tides   = .true.               !  Apply tidal harmonic forcing with Flather condition
+    ln_bdy_dyn_fla = .true.               !  Apply Flather condition to velocities
+    ln_bdy_tra_frs = .false.              !  Apply FRS condition to temperature and salinity
+    ln_bdy_dyn_frs = .false.              !  Apply FRS condition to velocities
+    nbdy_dta       =  1                   !  = 0, bdy data are equal to the initial state
+                                          !  = 1, bdy data are read in 'bdydata   .nc' files
+    nb_rimwidth    = 9                    !  width of the relaxation zone
+    volbdy         = 0                    !  = 0, the total water flux across open boundaries is zero
+                                          !  = 1, the total volume of the system is conserved
+   cn_mask       =  ''                    !  name of mask file (if ln_bdy_mask=.TRUE.)
+   cn_dta_frs_T  = 'bdydata_grid_T.nc'    !  name of data file (T-points)
+   cn_dta_frs_U  = 'bdydata_grid_U.nc'    !  name of data file (U-points)
+   cn_dta_frs_V  = 'bdydata_grid_V.nc'    !  name of data file (V-points)
+   cn_dta_fla_T  = 'bdydata_bt_grid_T.nc' !  name of data file for Flather condition (T-points)
+   cn_dta_fla_U  = 'bdydata_bt_grid_U.nc' !  name of data file for Flather condition (U-points)
+   cn_dta_fla_V  = 'bdydata_bt_grid_V.nc' !  name of data file for Flather condition (V-points)
+   ln_clim       = .false.                !  contain 1 (T) or 12 (F) time dumps and be cyclic
+   ln_vol        = .true.                 !  total volume correction (see volbdy parameter)
+   ln_mask       = .false.                !  boundary mask from filbdy_mask (T) or boundaries on edges of domain (F)
+   ln_tides      = .true.                 !  Apply tidal harmonic forcing with Flather condition
+   ln_dyn_fla    = .true.                 !  Apply Flather condition to velocities
+   ln_tra_frs    = .false.                !  Apply FRS condition to temperature and salinity
+   ln_dyn_frs    = .false.                !  Apply FRS condition to velocities
+   nn_rimwidth   =  9                     !  width of the relaxation zone
+   nn_dtactl     =  1                     !  bdy data read in 'bdydata_...nc' (=1) or set to the initial state (=0)
+   nn_volctl     =  0                     !  set to zero the net flux across open boundaries (=0) including E-P-R (=1)
+/

branches/nemo_v3_3_beta/DOC/TexFiles/Namelist/namsbc

-                      r2282
+                      r2349
    nn_fsbc     = 5         !  frequency of surface boundary condition computation
                            !               (= the frequency of sea-ice model call)
+   ln_ana      = .false.   !  analytical formulation (T => fill namsbc_ana )
+   ln_flx      = .false.   !  flux formulation       (T => fill namsbc_flx )
+   ln_blk_clio = .true.    !  CLIO bulk formulation  (T => fill namsbc_clio)
+   ln_blk_core = .false.   !  CORE bulk formulation  (T => fill namsbc_core)
+   ln_cpl      = .false.   !  Coupled formulation    (T => fill namsbc_cpl )
+   ln_ana      = .false.   !  analytical formulation                    (T => fill namsbc_ana )
+   ln_flx      = .false.   !  flux formulation                          (T => fill namsbc_flx )
+   ln_blk_clio = .true.    !  CLIO bulk formulation                     (T => fill namsbc_clio)
+   ln_blk_core = .false.   !  CORE bulk formulation                     (T => fill namsbc_core)
+   ln_cpl      = .false.   !  Coupled formulation                       (T => fill namsbc_cpl )
+   ln_apr_blk  = .false.   !  Patm used in bulk formulation             (T => fill namsbc_apr )
+   ln_apr_dyn  = .false.   !  Patm gradient added in ocean & ice Eqs.   (T => fill namsbc_apr )
    nn_ice      = 2         !  =0 no ice boundary condition   ,
                            !  =1 use observed ice-cover      ,
                            !  =2 ice-model used                             ("key_lim3" or "key_lim2)
+                           !  =2 ice-model used                         ("key_lim3" or "key_lim2)
    nn_ico_cpl  = 0         !  ice-ocean coupling : =0 each nn_fsbc
                            !                       =1 stresses recomputed each ocean time step ("key_lim3" only)
                            !                       =2 combination of 0 and 1 cases             ("key_lim3" only)
+                           !                       =1 stress recomputed each ocean time step ("key_lim3" only)
+                           !                       =2 combination of 0 and 1 cases           ("key_lim3" only)
    ln_dm2dc    = .false.   !  daily mean to diurnal cycle short wave (qsr)
    ln_rnf      = .true.    !  runoffs (T => fill namsbc_rnf)
    ln_ssr      = .true.    !  Sea Surface Restoring on T and/or S (T => fill namsbc_ssr)
+   ln_rnf      = .true.    !  runoffs                                   (T => fill namsbc_rnf)
+   ln_ssr      = .true.    !  Sea Surface Restoring on T and/or S       (T => fill namsbc_ssr)
    nn_fwb      = 3         !  FreshWater Budget: =0 unchecked
                            !                     =1 global mean of e-p-r set to zero at each time step
                            !                     =2 annual global mean of e-p-r set to zero
                            !                     =3 global emp set to zero and spread out over erp area
+                           !                     =1 set to zero at each time step
+                           !                     =2 set to zero in annual mean
+                           !                     =3 as in case 1 but spread out over erp area
+/

branches/nemo_v3_3_beta/DOC/TexFiles/Namelist/namzdf_gls

-                      r2298
+                      r2349
 &namzdf_gls                !   GLS vertical diffusion                   ("key_zdfgls")
 !-----------------------------------------------------------------------
    rn_emin     =   1.e-6   !  minimum value of e   [m2/s2]
    rn_epsmin   =   1.e-12  !  minimum value of eps [m2/s3]
+   rn_emin       = 1.e-6   !  minimum value of e   [m2/s2]
+   rn_epsmin     = 1.e-12  !  minimum value of eps [m2/s3]
    ln_length_lim = .true.  !  limit on the dissipation rate under stable stratification (Galperin et al., 1988)
    clim_galp   =   0.53    !  galperin limit
    ln_crban = .TRUE.       !  Use Craig & Banner (1994) surface wave mixing parametrisation
    ln_sigpsi = .TRUE.      !  Activate or not Burchard 2001 mods on psi schmidt number in the wb case
    rn_crban = 100.         !  Craig and Banner 1994 constant for wb tke flux
    rn_charn =  70000.      !  Charnock constant for wb induced roughness length
    nn_tkebc_surf  =   1    !  surface tke condition (0/1/2=Dir/Neum/Dir Mellor-Blumberg)
    nn_tkebc_bot   =   1    !  bottom tke condition (0/1=Dir/Neum)
    nn_psibc_surf  =   1    !  surface psi condition (0/1/2=Dir/Neum/Dir Mellor-Blumberg)
    nn_psibc_bot   =   1    !  bottom psi condition (0/1=Dir/Neum)
    nn_stab_func   =   2    !  stability function (0=Galp, 1= KC94, 2=CanutoA, 3=CanutoB)
    nn_clos        =   1    !  predefined closure type (0=MY82, 1=k-eps, 2=k-w, 3=Gen)
+   rn_clim_galp  = 0.53    !  galperin limit
+   ln_crban      = .true.  !  Use Craig & Banner (1994) surface wave mixing parametrisation
+   ln_sigpsi     = .true.  !  Activate or not Burchard 2001 mods on psi schmidt number in the wb case
+   rn_crban      = 100.    !  Craig and Banner 1994 constant for wb tke flux
+   rn_charn      = 70000.  !  Charnock constant for wb induced roughness length
+   nn_tkebc_surf = 1       !  surface tke condition (0/1/2=Dir/Neum/Dir Mellor-Blumberg)
+   nn_tkebc_bot  = 1       !  bottom tke condition (0/1=Dir/Neum)
+   nn_psibc_surf = 1       !  surface psi condition (0/1/2=Dir/Neum/Dir Mellor-Blumberg)
+   nn_psibc_bot  = 1       !  bottom psi condition (0/1=Dir/Neum)
+   nn_stab_func  = 2       !  stability function (0=Galp, 1= KC94, 2=CanutoA, 3=CanutoB)
+   nn_clos       = 1       !  predefined closure type (0=MY82, 1=k-eps, 2=k-w, 3=Gen)
+/

branches/nemo_v3_3_beta/DOC/TexFiles/math_abbrev.sty

r2285	r2349
12	12	\newcommand{\ew}[3]{{e_{3#1}}_{\,#2}^{\,#3} }
13	13	\newcommand{\vect}[1]{ \rm{\textbf{#1}} } % vector style: non-italic bold
	14	\def\deg{\degres} % degrees (NB: \r{} can also be used)

New URL for NEMO forge! http://forge.nemo-ocean.eu

Context Navigation

Legend:

branches/nemo_v3_3_beta/DOC/TexFiles/Biblio/Biblio.bib

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Annex_D.tex

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_ASM.tex

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_DOM.tex

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_DYN.tex

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_LBC.tex

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_LDF.tex

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_MISC.tex

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_Model_Basics.tex

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_OBS.tex

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_SBC.tex

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_TRA.tex

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_ZDF.tex

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Introduction.tex

branches/nemo_v3_3_beta/DOC/TexFiles/Namelist/namasm

branches/nemo_v3_3_beta/DOC/TexFiles/Namelist/nambdy

branches/nemo_v3_3_beta/DOC/TexFiles/Namelist/namsbc

branches/nemo_v3_3_beta/DOC/TexFiles/Namelist/namzdf_gls

branches/nemo_v3_3_beta/DOC/TexFiles/math_abbrev.sty

Download in other formats: