Changeset 14789 for NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU

Property svn:externals

-                      old
+                      new
 ^/utils/build/mk@HEAD         mk
 ^/utils/tools@HEAD            tools
 ^/vendors/AGRIF/dev_r12970_AGRIF_CMEMS      ext/AGRIF
+^/vendors/AGRIF/dev@HEAD      ext/AGRIF
 ^/vendors/FCM@HEAD            ext/FCM
 ^/vendors/IOIPSL@HEAD         ext/IOIPSL
+^/vendors/PPR@HEAD            ext/PPR
 # SETTE
 ^/utils/CI/sette@13559        sette
+^/utils/CI/sette@14244        sette

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles

Property svn:ignore

-                      old
+                      new
+*.aux
+*.bbl
+*.blg
+*.fdb*
+*.fls
+*.idx
+*.ilg
 *.ind
+*.ilg
+*.lo*
+*.out
+*.pdf
+*.pyg
+*.tdo
+*.toc
+*.xdv
+cache*

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex

-                      r11693
+                      r14789
 \label{apdx:DOMCFG}
-%    {\em 4.0} & {\em Andrew Coward} & {\em Created at v4.0 from materials removed from chap\_DOM that are still relevant to the \forcode{DOMAINcfg} tool and which illustrate and explain the choices to be made by the user when setting up new domains }  \\
-\thispagestyle{plain}
 \chaptertoc
 …
 {\footnotesize
   \begin{tabularx}{\textwidth}{l||X|X}
     Release & Author(s) & Modifications \\
     \hline
     {\em   4.0} & {\em ...} & {\em ...} \\
     {\em   3.6} & {\em ...} & {\em ...} \\
     {\em   3.4} & {\em ...} & {\em ...} \\
     {\em <=3.4} & {\em ...} & {\em ...}
+    Release     & Author(s)            & Modifications                                                 \\
+    \hline
+    {\em  next} & {\em Pierre Mathiot} & {\em Add ice shelf and closed sea option description        } \\
+    {\em   4.0} & {\em  Andrew Coward} & {\em Creation from materials removed from \autoref{chap:DOM}
+                                              that are still relevant to the DOMAINcfg tool
+                                              when setting up new domains                            }
   \end{tabularx}
+}
 …
 \begin{listing}
+  \nlst{namdom_domcfg}
+  \begin{forlines}
+!-----------------------------------------------------------------------
+&namdom        !   space and time domain (bathymetry, mesh, timestep)
+!-----------------------------------------------------------------------
+   nn_bathy    =    1      !  compute analyticaly (=0) or read (=1) the bathymetry file
+                           !  or compute (2) from external bathymetry
+   nn_interp   =    1                          ! type of interpolation (nn_bathy =2)
+   cn_topo     =  'bathymetry_ORCA12_V3.3.nc'  ! external topo file (nn_bathy =2)
+   cn_bath     =  'Bathymetry'                 ! topo name in file  (nn_bathy =2)
+   cn_lon      =  'nav_lon'                    ! lon  name in file  (nn_bathy =2)
+   cn_lat      =  'nav_lat'                    ! lat  name in file  (nn_bathy =2)
+   rn_scale    = 1
+   rn_bathy    =    0.     !  value of the bathymetry. if (=0) bottom flat at jpkm1
+   jphgr_msh   =       0               !  type of horizontal mesh
+   ppglam0     =  999999.0             !  longitude of first raw and column T-point (jphgr_msh = 1)
+   ppgphi0     =  999999.0             ! latitude  of first raw and column T-point (jphgr_msh = 1)
+   ppe1_deg    =  999999.0             !  zonal      grid-spacing (degrees)
+   ppe2_deg    =  999999.0             !  meridional grid-spacing (degrees)
+   ppe1_m      =  999999.0             !  zonal      grid-spacing (degrees)
+   ppe2_m      =  999999.0             !  meridional grid-spacing (degrees)
+   ppsur       =   -4762.96143546300   !  ORCA r4, r2 and r05 coefficients
+   ppa0        =     255.58049070440   ! (default coefficients)
+   ppa1        =     245.58132232490   !
+   ppkth       =      21.43336197938   !
+   ppacr       =       3.0             !
+   ppdzmin     =  999999.              !  Minimum vertical spacing
+   pphmax      =  999999.              !  Maximum depth
+   ldbletanh   =  .FALSE.              !  Use/do not use double tanf function for vertical coordinates
+   ppa2        =  999999.              !  Double tanh function parameters
+   ppkth2      =  999999.              !
+   ppacr2      =  999999.              !
+/
+  \end{forlines}
   \caption{\forcode{&namdom_domcfg}}
   \label{lst:namdom_domcfg}
 …
  \item [{\np{jphgr_mesh}{jphgr\_mesh}=0}]  The most general curvilinear orthogonal grids.
   The coordinates and their first derivatives with respect to $i$ and $j$ are provided
   in a input file (\ifile{coordinates}), read in \rou{hgr\_read} subroutine of the domhgr module.
+  in a input file (\textit{coordinates.nc}), read in \rou{hgr\_read} subroutine of the domhgr module.
   This is now the only option available within \NEMO\ itself from v4.0 onwards.
 \item [{\np{jphgr_mesh}{jphgr\_mesh}=1 to 5}] A few simple analytical grids are provided (see below).
 …
 The reference coordinate transformation $z_0(k)$ defines the arrays $gdept_0$ and
 $gdepw_0$ for $t$- and $w$-points, respectively. See \autoref{sec:DOMCFG_sco} for the
 S-coordinate options.  As indicated on \autoref{fig:DOM_index_vert} \jp{jpk} is the number of
 $w$-levels.  $gdepw_0(1)$ is the ocean surface.  There are at most \jp{jpk}-1 $t$-points
+S-coordinate options.  As indicated on \autoref{fig:DOM_index_vert} \texttt{jpk} is the number of
+$w$-levels.  $gdepw_0(1)$ is the ocean surface.  There are at most \texttt{jpk}-1 $t$-points
 inside the ocean, the additional $t$-point at $jk = jpk$ is below the sea floor and is not
 used.  The vertical location of $w$- and $t$-levels is defined from the analytic
 …
 It is possible to define a simple regular vertical grid by giving zero stretching
 (\np[=0]{ppacr}{ppacr}).  In that case, the parameters \jp{jpk} (number of $w$-levels)
+(\np[=0]{ppacr}{ppacr}).  In that case, the parameters \texttt{jpk} (number of $w$-levels)
 and \np{pphmax}{pphmax} (total ocean depth in meters) fully define the grid.
 …
 \end{gather}
 where $k = 1$ to \jp{jpk} for $w$-levels and $k = 1$ to $k = 1$ for $t-$levels.  Such an
+where $k = 1$ to \texttt{jpk} for $w$-levels and $k = 1$ to $k = 1$ for $t-$levels.  Such an
 expression allows us to define a nearly uniform vertical location of levels at the ocean
 top and bottom with a smooth hyperbolic tangent transition in between (\autoref{fig:DOMCFG_zgr}).
 …
 \end{equation}
 With the choice of the stretching $h_{cr} = 3$ and the number of levels \jp{jpk}~$= 31$,
+With the choice of the stretching $h_{cr} = 3$ and the number of levels \texttt{jpk}~$= 31$,
 the four coefficients $h_{sur}$, $h_0$, $h_1$, and $h_{th}$ in
 \autoref{eq:DOMCFG_zgr_ana_2} have been determined such that \autoref{eq:DOMCFG_zgr_coef}
 …
   Values from $3$ to $10$ are usual.
 \item \np{ppkth}{ppkth}~$= h_{th}$: is approximately the model level at which maximum stretching occurs
   (nondimensional, usually of order 1/2 or 2/3 of \jp{jpk})
+  (nondimensional, usually of order 1/2 or 2/3 of \texttt{jpk})
 \item \np{ppdzmin}{ppdzmin}: minimum thickness for the top layer (in meters).
 \item \np{pphmax}{pphmax}: total depth of the ocean (meters).
 …
 As an example, for the $45$ layers used in the DRAKKAR configuration those parameters are:
 \jp{jpk}~$= 46$, \np{ppacr}{ppacr}~$= 9$, \np{ppkth}{ppkth}~$= 23.563$, \np{ppdzmin}{ppdzmin}~$= 6~m$,
+\texttt{jpk}~$= 46$, \np{ppacr}{ppacr}~$= 9$, \np{ppkth}{ppkth}~$= 23.563$, \np{ppdzmin}{ppdzmin}~$= 6~m$,
 \np{pphmax}{pphmax}~$= 5750~m$.
 …
   This is meant for the "EEL-R5" configuration, a periodic or open boundary channel with a seamount.
 \item [{\np[=1]{nn_bathy}{nn\_bathy}}]: read a bathymetry and ice shelf draft (if needed).
   The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters) at
+  The \textit{bathy\_meter.nc} file (Netcdf format) provides the ocean depth (positive, in meters) at
   each grid point of the model grid.
   The bathymetry is usually built by interpolating a standard bathymetry product (\eg\ ETOPO2) onto
 …
   Defining the bathymetry also defines the coastline: where the bathymetry is zero,
   no wet levels are defined (all levels are masked).
-  The \ifile{isfdraft\_meter} file (Netcdf format) provides the ice shelf draft (positive, in meters) at
-  each grid point of the model grid.
-  This file is only needed if \np[=.true.]{ln_isfcav}{ln\_isfcav}.
-  Defining the ice shelf draft will also define the ice shelf edge and the grounding line position.
 \end{description}
 …
 bathymetry varies by less than one level thickness from one grid point to the next).  The
 reference layer thicknesses $e_{3t}^0$ have been defined in the absence of bathymetry.
 With partial steps, layers from 1 to \jp{jpk}-2 can have a thickness smaller than
+With partial steps, layers from 1 to \texttt{jpk-2} can have a thickness smaller than
 $e_{3t}(jk)$.
 The model deepest layer (\jp{jpk}-1) is allowed to have either a smaller or larger
+The model deepest layer (\texttt{jpk-1}) is allowed to have either a smaller or larger
 thickness than $e_{3t}(jpk)$: the maximum thickness allowed is $2*e_{3t}(jpk - 1)$.
 …
 \subsubsection[$S$-coordinate (\forcode{ln_sco})]{$S$-coordinate (\protect\np{ln_sco}{ln\_sco})}
 \label{sec:DOMCFG_sco}
 \begin{listing}
-  \nlst{namzgr_sco_domcfg}
   \caption{\forcode{&namzgr_sco_domcfg}}
   \label{lst:namzgr_sco_domcfg}
+  \begin{forlines}
+!-----------------------------------------------------------------------
+&namzgr_sco    !   s-coordinate or hybrid z-s-coordinate                (default: OFF)
+!-----------------------------------------------------------------------
+   ln_s_sh94   = .false.    !  Song & Haidvogel 1994 hybrid S-sigma   (T)|
+   ln_s_sf12   = .false.   !  Siddorn & Furner 2012 hybrid S-z-sigma (T)| if both are false the NEMO tanh stretching is applied
+   ln_sigcrit  = .false.   !  use sigma coordinates below critical depth (T) or Z coordinates (F) for Siddorn & Furner stretch
+                           !  stretching coefficients for all functions
+   rn_sbot_min =   10.0    !  minimum depth of s-bottom surface (>0) (m)
+   rn_sbot_max = 7000.0    !  maximum depth of s-bottom surface (= ocean depth) (>0) (m)
+   rn_hc       =  150.0    !  critical depth for transition to stretched coordinates
+                        !!!!!!!  Envelop bathymetry
+   rn_rmax     =    0.3    !  maximum cut-off r-value allowed (0<r_max<1)
+                        !!!!!!!  SH94 stretching coefficients  (ln_s_sh94 = .true.)
+   rn_theta    =    6.0    !  surface control parameter (0<=theta<=20)
+   rn_bb       =    0.8    !  stretching with SH94 s-sigma
+                        !!!!!!!  SF12 stretching coefficient  (ln_s_sf12 = .true.)
+   rn_alpha    =    4.4    !  stretching with SF12 s-sigma
+   rn_efold    =    0.0    !  efold length scale for transition to stretched coord
+   rn_zs       =    1.0    !  depth of surface grid box
+                           !  bottom cell depth (Zb) is a linear function of water depth Zb = H*a + b
+   rn_zb_a     =    0.024  !  bathymetry scaling factor for calculating Zb
+   rn_zb_b     =   -0.2    !  offset for calculating Zb
+                        !!!!!!!! Other stretching (not SH94 or SF12) [also uses rn_theta above]
+   rn_thetb    =    1.0    !  bottom control parameter  (0<=thetb<= 1)
+/
+  \end{forlines}
 \end{listing}
+Options are defined in \nam{zgr_sco}{zgr\_sco} (\texttt{DOMAINcfg} only).
+Options are defined in \forcode{&zgr_sco} (\texttt{DOMAINcfg} only).
 In $s$-coordinate (\np[=.true.]{ln_sco}{ln\_sco}), the depth and thickness of the model levels are defined from
 the product of a depth field and either a stretching function or its derivative, respectively:
 …
 This option is described in the Report by Levier \textit{et al.} (2007), available on the \NEMO\ web site.
+\section{Ice shelf cavity definition}
+\label{subsec:zgrisf}
+  If the under ice shelf seas are opened (\np{ln_isfcav}{ln\_isfcav}), the depth of the ice shelf/ocean interface has to be include in
+  the \textit{isfdraft\_meter} file (Netcdf format). This file need to include the \textit{isf\_draft} variable.
+  A positive value will mean ice shelf/ocean or ice shelf bedrock interface below the reference 0m ssh.
+  The exact shape of the ice shelf cavity (grounding line position and minimum thickness of the water column under an ice shelf, ...) can be specify in \nam{zgr_isf}{zgr\_isf}.
+\begin{listing}
+  \caption{\forcode{&namzgr_isf}}
+  \label{lst:namzgr_isf}
+  \begin{forlines}
+!-----------------------------------------------------------------------
+&namzgr_isf    !   isf cavity geometry definition                       (default: OFF)
+!-----------------------------------------------------------------------
+   rn_isfdep_min    = 10.         ! minimum isf draft tickness (if lower, isf draft set to this value)
+   rn_glhw_min      = 1.e-3       ! minimum water column thickness to define the grounding line
+   rn_isfhw_min     = 10          ! minimum water column thickness in the cavity once the grounding line defined.
+   ln_isfchannel    = .false.     ! remove channel (based on 2d mask build from isfdraft-bathy)
+   ln_isfconnect    = .false.     ! force connection under the ice shelf (based on 2d mask build from isfdraft-bathy)
+      nn_kisfmax       = 999         ! limiter in level on the previous condition. (if change larger than this number, get back to value before we enforce the connection)
+      rn_zisfmax       = 7000.       ! limiter in m     on the previous condition. (if change larger than this number, get back to value before we enforce the connection)
+   ln_isfcheminey   = .false.     ! close cheminey
+   ln_isfsubgl      = .false.     ! remove subglacial lake created by the remapping process
+      rn_isfsubgllon   =    0.0      !  longitude of the seed to determine the open ocean
+      rn_isfsubgllat   =    0.0      !  latitude  of the seed to determine the open ocean
+/
+  \end{forlines}
+\end{listing}
+   The options available to define the shape of the under ice shelf cavities are listed in \nam{zgr_isf}{zgr\_isf} (\texttt{DOMAINcfg} only, \autoref{lst:namzgr_isf}).
+\subsection{Model ice shelf draft definition}
+\label{subsec:zgrisf_isfd}
+First of all, the tool make sure, the ice shelf draft ($h_{isf}$) is sensible and compatible with the bathymetry.
+There are 3 compulsory steps to achieve this:
+\begin{description}
+\item{\np{rn_isfdep_min}{rn\_isfdep\_min}:} this is the minimum ice shelf draft. This is to make sure there is no ridiculous thin ice shelf. If \np{rn_isfdep_min}{rn\_isfdep\_min} is smaller than the surface level, \np{rn_isfdep_min}{rn\_isfdep\_min} is set to $e3t\_1d(1)$.
+  Where $h_{isf} < MAX(e3t\_1d(1),rn\_isfdep\_min)$, $h_{isf}$ is set to \np{rn_isfdep_min}{rn\_isfdep\_min}.
+\item{\np{rn_glhw_min}{rn\_glhw\_min}:} This parameter is used to define the grounding line position.
+  Where the difference between the bathymetry and the ice shelf draft is smaller than \np{rn_glhw_min}{rn\_glhw\_min}, the cell are grounded (ie masked).
+  This step is needed to take into account possible small mismatch between ice shelf draft value and bathymetry value (sources are coming from different grid, different data processes, rounding error, ...).
+\item{\np{rn_isfhw_min}{rn\_isfhw\_min}:} This parameter is the minimum water column thickness in the cavity.
+  Where the water column thickness is lower than \np{rn_isfhw_min}{rn\_isfhw\_min}, the ice shelf draft is adjusted to match this criterion.
+  If for any reason, this adjustement break the minimum ice shelf draft allowed (\np{rn_isfdep_min}{rn\_isfdep\_min}), the cell is masked.
+\end{description}
+Once all these adjustements are made, if the water column thickness contains one cell wide channels, these channels can be closed using \np{ln_isfchannel}{ln\_isfchannel}.
+\subsection{Model top level definition}
+After the definition of the ice shelf draft, the tool defines the top level.
+The compulsory criterion is that the water column needs at least 2 wet cells in the water column at U- and V-points.
+To do so, if there one cell wide water column, the tools adjust the ice shelf draft to fillful the requierement.\\
+The process is the following:
+\begin{description}
+\item{step 1:} The top level is defined in the same way as the bottom level is defined.
+\item{step 2:} The isolated grid point in the bathymetry are filled (as it is done in a domain without ice shelf)
+\item{step 3:} The tools make sure, the top level is above or equal to the bottom level
+\item{step 4:} If the water column at a U- or V- point is one wet cell wide, the ice shelf draft is adjusted. So the actual top cell become fully open and the new
+  top cell thickness is set to the minimum cell thickness allowed (following the same logic as for the bottom partial cell). This step is iterated 4 times to ensure the condition is fullfill along the 4 sides of the cell.
+\end{description}
+In case of steep slope and shallow water column, it likely that 2 cells are disconnected (bathymetry above its neigbourging ice shelf draft).
+The option \np{ln_isfconnect}{ln\_isfconnect} allow the tool to force the connection between these 2 cells.
+Some limiters in meter or levels on the digging allowed by the tool are available (respectively, \np{rn_zisfmax}{rn\_zisfmax} or \np{rn_kisfmax}{rn\_kisfmax}).
+This will prevent the formation of subglacial lakes at the expense of long vertical pipe to connect cells at very different levels.
+\subsection{Subglacial lakes}
+Despite careful setting of your ice shelf draft and bathymetry input file as well as setting described in \autoref{subsec:zgrisf_isfd}, some situation are unavoidable.
+For exemple if you setup your ice shelf draft and bathymetry to do ocean/ice sheet coupling,
+you may decide to fill the whole antarctic with a bathymetry and an ice shelf draft value (ice/bedrock interface depth when grounded).
+If you do so, the subglacial lakes will show up (Vostock for example). An other possibility is with coarse vertical resolution, some ice shelves could be cut in 2 parts:
+one connected to the main ocean and an other one closed which can be considered as a subglacial sea be the model.\\
+The namelist option \np{ln_isfsubgl}{ln\_isfsubgl} allow you to remove theses subglacial lakes.
+This may be useful for esthetical reason or for stability reasons:
+\begin{description}
+\item $\bullet$ In a subglacial lakes, in case of very weak circulation (often the case), the only heat flux is the conductive heat flux through the ice sheet.
+  This will lead to constant freezing until water reaches -20C.
+  This is one of the defitiency of the 3 equation melt formulation (for details on this formulation, see: \autoref{sec:isf}).
+\item $\bullet$ In case of coupling with an ice sheet model,
+  the ssh in the subglacial lakes and the main ocean could be very different (ssh initial adjustement for example),
+  and so if for any reason both a connected at some point, the model is likely to fall over.\\
+\end{description}
+\section{Closed sea definition}
+\label{sec:clocfg}
+\begin{listing}
+  \caption{\forcode{&namclo}}
+  \label{lst:namdom_clo}
+  \begin{forlines}
+!-----------------------------------------------------------------------
+&namclo ! (closed sea : need ln_domclo = .true. in namcfg)
+!-----------------------------------------------------------------------
+   rn_lon_opnsea = -2.0     ! longitude seed of open ocean
+   rn_lat_opnsea = -2.0     ! latitude  seed of open ocean
+   nn_closea = 8           ! number of closed seas ( = 0; only the open_sea mask will be computed)
+   !                name   ! lon_src ! lat_src ! lon_trg ! lat_trg ! river mouth area   ! net evap/precip correction scheme ! radius tgt   ! id trg
+   !                       ! (degree)! (degree)! (degree)! (degree)! local/coast/global ! (glo/rnf/emp)                     !     (m)      !
+   ! North American lakes
+   sn_lake(1) = 'superior' ,  -86.57 ,  47.30  , -66.49  , 50.45   , 'local'            , 'rnf'                             ,   550000.0 , 2
+   sn_lake(2) = 'michigan' ,  -87.06 ,  42.74  , -66.49  , 50.45   , 'local'            , 'rnf'                             ,   550000.0 , 2
+   sn_lake(3) = 'huron'    ,  -82.51 ,  44.74  , -66.49  , 50.45   , 'local'            , 'rnf'                             ,   550000.0 , 2
+   sn_lake(4) = 'erie'     ,  -81.13 ,  42.25  , -66.49  , 50.45   , 'local'            , 'rnf'                             ,   550000.0 , 2
+   sn_lake(5) = 'ontario'  ,  -77.72 ,  43.62  , -66.49  , 50.45   , 'local'            , 'rnf'                             ,   550000.0 , 2
+   ! African Lake
+   sn_lake(6) = 'victoria' ,   32.93 ,  -1.08  ,  30.44  , 31.37   , 'coast'            , 'emp'                             ,   100000.0 , 3
+   ! Asian Lakes
+   sn_lake(7) = 'caspian'  ,   50.0  ,  44.0   ,   0.0   ,  0.0    , 'global'           , 'glo'                             ,        0.0 , 1
+   sn_lake(8) = 'aral'     ,   60.0  ,  45.0   ,   0.0   ,  0.0    , 'global'           , 'glo'                             ,        0.0 , 1
+/
+   \end{forlines}
+\end{listing}
+The options available to define the closed seas and how closed sea net fresh water input will be redistributed by NEMO are listed in \nam{dom_clo}{dom\_clo} (\texttt{DOMAINcfg} only).
+The individual definition of each closed sea is managed by \np{sn_lake}{sn\_lake}. In this fields the user needs to define:\\
+   \begin{description}
+   \item $\bullet$    the name of the closed sea (print output purposes).
+   \item $\bullet$    the seed location to define the area of the closed sea (if seed on land because not present in this configuration, this closed sea will be ignored).\\
+   \item $\bullet$    the seed location for the target area.
+   \item $\bullet$    the type of target area ('local','coast' or 'global'). See point 6 for definition of these cases.
+   \item $\bullet$    the type of redistribution scheme for the net fresh water flux over the closed sea (as a runoff in a target area, as emp in a target area, as emp globally). For the runoff case, if the net fwf is negative, it will be redistribut globally.
+   \item $\bullet$    the radius of the target area (not used for the 'global' case). So the target defined by a 'local' target area of a radius of 100km, for example, correspond to all the wet points within this radius. The coastal case will return only the coastal point within the specifid radius.
+   \item $\bullet$    the target id. This target id is used to group multiple lakes into the same river ouflow (Great Lakes for example).
+   \end{description}
+The closed sea module defines a number of masks in the \textit{domain\_cfg} output:
+   \begin{description}
+   \item[\textit{mask\_opensea}:] a mask of the main ocean without all the closed seas closed. This mask is defined by a flood filling algorithm with an initial seed (localisation defined by \np{rn_lon_opnsea}{rn\_lon\_opnsea} and \np{rn_lat_opnsea}{rn\_lat\_opnsea}).
+   \item[\textit{mask\_csglo}, \textit{mask\_csrnf}, \textit{mask\_csemp}:] a mask of all the closed seas defined in the namelist by \np{sn_lake}{sn\_lake} for each redistribution scheme. The total number of defined closed seas has to be defined in \np{nn_closea}{nn\_closea}.
+   \item[\textit{mask\_csgrpglo}, \textit{mask\_csgrprnf}, \textit{mask\_csgrpemp}:] a mask of all the closed seas and targets grouped by target id for each type of redistribution scheme.
+   \item[\textit{mask\_csundef}:] a mask of all the closed sea not defined in \np{sn_lake}{sn\_lake}. This will allows NEMO to mask them if needed or to inform the user of potential minor issues in its bathymetry.
+   \end{description}
 \subinc{\input{../../global/epilogue}}

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5	5	\chapter{Note on some algorithms}
6	6	\label{apdx:ALGOS}
7
8		~~\thispagestyle{plain}~~
9	7
10	8	\chaptertoc

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5	5	\chapter{Diffusive Operators}
6	6	\label{apdx:DIFFOPERS}
7
8		~~\thispagestyle{plain}~~
9	7
10	8	\chaptertoc

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5	5	\chapter{Discrete Invariants of the Equations}
6	6	\label{apdx:INVARIANTS}
7
8		~~\thispagestyle{plain}~~
9	7
10	8	\chaptertoc

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/apdx_s_coord.tex

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8	8	% {\em 4.0} & {\em Mike Bell} & {\em review} \\
9	9	% {\em 3.x} & {\em Gurvan Madec} & {\em original} \\
10
11		~~\thispagestyle{plain}~~
12	10
13	11	\chaptertoc

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/apdx_triads.tex

-                      r11693
+                      r14789
 \documentclass[../main/NEMO_manual]{subfiles}
-%% Local cmds
-\newcommand{\rML}[1][i]{\ensuremath{_{\mathrm{ML}\,#1}}}
-\newcommand{\rMLt}[1][i]{\tilde{r}_{\mathrm{ML}\,#1}}
-%% Move to ../../global/new_cmds.tex to avoid error with \listoffigures
-%\newcommand{\triad}[6][]{\ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}}
-\newcommand{\triadd}[5]{\ensuremath{{}_{#1}^{#2}{\mathbb{#3}}_{#4}^{\,#5}}}
-\newcommand{\triadt}[5]{\ensuremath{{}_{#1}^{#2}{\tilde{\mathbb{#3}}}_{#4}^{\,#5}}}
-\newcommand{\rtriad}[2][]{\ensuremath{\triad[#1]{i}{k}{#2}{i_p}{k_p}}}
-\newcommand{\rtriadt}[1]{\ensuremath{\triadt{i}{k}{#1}{i_p}{k_p}}}
 \begin{document}
 …
 \chapter{Iso-Neutral Diffusion and Eddy Advection using Triads}
 \label{apdx:TRIADS}
-\thispagestyle{plain}
 \chaptertoc
 …
 %% =================================================================================================
 \section[Choice of \forcode{namtra\_ldf} namelist parameters]{Choice of \protect\nam{tra_ldf}{tra\_ldf} namelist parameters}
+\section[Choice of \forcode{namtra_ldf} namelist parameters]{Choice of \protect\nam{tra_ldf}{tra\_ldf} namelist parameters}
 Two scheme are available to perform the iso-neutral diffusion.

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_ASM.tex

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8	8	% {\em 4.0} & {\em D. J. Lea} & {\em \NEMO\ 4.0 updates} \\
9	9	% {\em 3.4} & {\em D. J. Lea, M. Martin, K. Mogensen, A. Weaver} & {\em Initial version} \\
10
11		~~\thispagestyle{plain}~~
12	10
13	11	\chaptertoc

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_DIA.tex

-                      r12377
+                      r14789
 %    {\em 3.4} & {\em Gurvan Madec, Rachid Benshila, Andrew Coward } & {\em }  \\
 %    {\em }      & {\em Christian Ethe, Sebastien Masson } & {\em }  \\
-\thispagestyle{plain}
 \chaptertoc
 …
 \subsection{XIOS: Reading and writing restart file}
+XIOS may be used to read single file restart produced by \NEMO. Currently only the variables written to
+file \forcode{numror} can be handled by XIOS. To activate restart reading using XIOS, set \np[=.true. ]{ln_xios_read}{ln\_xios\_read}
+XIOS may be used to read single file restart produced by \NEMO. The variables written to
+file \forcode{numror} (OCE), \forcode{numrir} (SI3), \forcode{numrtr} (TOP), \forcode{numrsr} (SED) can be handled by XIOS.
+To activate restart reading using XIOS, set \np[=.true. ]{ln_xios_read}{ln\_xios\_read}
 in \textit{namelist\_cfg}. This setting will be ignored when multiple restart files are present, and default \NEMO
 functionality will be used for reading. There is no need to change iodef.xml file to use XIOS to read
 …
 have to be rebuild before continuing the run. This option aims to reduce number of restart files generated by \NEMO\ only,
 and may be useful when there is a need to change number of processors used to run simulation.
-If an additional variable must be written to a restart file, the following steps are needed:
-\begin{enumerate}
-\item Add variable name to a list of restart variables (in subroutine \rou{iom\_set\_rst\_vars,} \mdl{iom}) and
-define correct grid for the variable (\forcode{grid_N_3D} - 3D variable, \forcode{grid_N} - 2D variable, \forcode{grid_vector} -
-D variable, \forcode{grid_scalar} - scalar),
-\item Add variable to the list of fields written by restart.  This can be done either in subroutine
-\rou{iom\_set\_rstw\_core} (\mdl{iom}) or by calling  \rou{iom\_set\_rstw\_active} (\mdl{iom}) with the name of a variable
-as an argument. This convention follows approach for writing restart using iom, where variables are
-written either by \rou{rst\_write} or by calling \rou{iom\_rstput} from individual routines.
-\end{enumerate}
 An older versions of XIOS do not support reading functionality. It's recommended to use at least XIOS2@1451.
 …
 \end{forlines}
 \noindent will give the following file name radical: \ifile{myfile\_ORCA2\_19891231\_freq1d}
+\noindent will give the following file name radical: \textit{myfile\_ORCA2\_19891231\_freq1d}
 %% =================================================================================================
 …
 When \np[=.true.]{ln_subbas}{ln\_subbas}, 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 sub-basin decomposition requires an input file (\textit{subbasins}) which contains three 2D mask arrays,
 the Indo-Pacific mask been deduced from the sum of the Indian and Pacific mask (\autoref{fig:DIA_mask_subasins}).
 \begin{listing}
   \nlst{namptr}
+%  \nlst{namptr}
   \caption{\forcode{&namptr}}
   \label{lst:namptr}

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_DIU.tex

-                      r11693
+                      r14789
 \chapter{Diurnal SST Models (DIU)}
 \label{chap:DIU}
-\thispagestyle{plain}
 \chaptertoc
 …
 This namelist contains only two variables:
 \begin{description}
 \item [{\np{ln_diurnal}{ln\_diurnal}}] A logical switch for turning on/off both the cool skin and warm layer.

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_DOM.tex

-                      r11693
+                      r14789
 % -    domclo: closed sea and lakes....
 %              management of closea sea area: specific to global cfg, both forced and coupled
-\thispagestyle{plain}
 \chaptertoc
 …
 \label{subsec:DOM_size}
 The total size of the computational domain is set by the parameters \jp{jpiglo}, \jp{jpjglo} and
 \jp{jpkglo} for the $i$, $j$ and $k$ directions, respectively.
+The total size of the computational domain is set by the parameters \texttt{jpiglo}, \texttt{jpjglo} and
+\texttt{jpkglo} for the $i$, $j$ and $k$ directions, respectively.
 Note, that the variables \texttt{jpi} and \texttt{jpj} refer to
 the size of each processor subdomain when the code is run in parallel using domain decomposition
 …
 in which case \np{cn_cfg}{cn\_cfg} and \np{nn_cfg}{nn\_cfg} are set from these values accordingly).
 The global lateral boundary condition type is selected from 8 options using parameter \jp{jperio}.
+The global lateral boundary condition type is selected from 8 options using parameters \texttt{l\_Iperio}, \texttt{l\_Jperio}, \texttt{l\_NFold} and \texttt{c\_NFtype}.
 See \autoref{sec:LBC_jperio} for details on the available options and
 the corresponding values for \jp{jperio}.
+the corresponding values for \texttt{l\_Iperio}, \texttt{l\_Jperio}, \texttt{l\_NFold} and \texttt{c\_NFtype}.
 %% =================================================================================================
 …
 \begin{clines}
+int    jpiglo, jpjglo, jpkglo     /* global domain sizes                                    */
+int    jperio                     /* lateral global domain b.c.                             */
+double glamt, glamu, glamv, glamf /* geographic longitude (t,u,v and f points respectively) */
+double gphit, gphiu, gphiv, gphif /* geographic latitude                                    */
+double e1t, e1u, e1v, e1f         /* horizontal scale factors                               */
+double e2t, e2u, e2v, e2f         /* horizontal scale factors                               */
+integer   Ni0glo, NjOglo, jpkglo       /* global domain sizes (without MPI halos)                */
+logical   l\_Iperio, l\_Jperio         /* lateral global domain b.c.: i- j-periodicity           */
+logical   l\_NFold                     /* lateral global domain b.c.: North Pole folding         */
+char(1)   c\_NFtype                    /*    type of North pole Folding: T or F point            */
+real      glamt, glamu, glamv, glamf   /* geographic longitude (t,u,v and f points respectively) */
+real      gphit, gphiu, gphiv, gphif   /* geographic latitude                                    */
+real      e1t, e1u, e1v, e1f           /* horizontal scale factors                               */
+real      e2t, e2u, e2v, e2f           /* horizontal scale factors                               */
 \end{clines}
 …
 \begin{enumerate}
 \item the bathymetry given in meters;
 \item the number of levels of the model (\jp{jpk});
+\item the number of levels of the model (\texttt{jpk});
 \item the analytical transformation $z(i,j,k)$ and the vertical scale factors
   (derivatives of the transformation); and
 …
 every gridcell in the model regardless of the choice of vertical coordinate.
 With constant z-levels, e3 metrics will be uniform across each horizontal level.
 In the partial step case each e3 at the \jp{bottom\_level}
 (and, possibly, \jp{top\_level} if ice cavities are present)
+In the partial step case each e3 at the \texttt{bottom\_level}
+(and, possibly, \texttt{top\_level} if ice cavities are present)
 may vary from its horizontal neighbours.
 And, in s-coordinates, variations can occur throughout the water column.
 …
 those arising from a flat sea surface with zero elevation.
 The \jp{bottom\_level} and \jp{top\_level} 2D arrays define
 the \jp{bottom\_level} and top wet levels in each grid column.
 Without ice cavities, \jp{top\_level} is essentially a land mask (0 on land; 1 everywhere else).
 With ice cavities, \jp{top\_level} determines the first wet point below the overlying ice shelf.
+The \texttt{bottom\_level} and \texttt{top\_level} 2D arrays define
+the \texttt{bottom\_level} and top wet levels in each grid column.
+Without ice cavities, \texttt{top\_level} is essentially a land mask (0 on land; 1 everywhere else).
+With ice cavities, \texttt{top\_level} determines the first wet point below the overlying ice shelf.
 %% =================================================================================================
 …
 \label{subsec:DOM_msk}
 From \jp{top\_level} and \jp{bottom\_level} fields, the mask fields are defined as follows:
+From \texttt{top\_level} and \texttt{bottom\_level} fields, the mask fields are defined as follows:
 \begin{align*}
   tmask(i,j,k) &=

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_DYN.tex

-                      r11693
+                      r14789
 \chapter{Ocean Dynamics (DYN)}
 \label{chap:DYN}
-\thispagestyle{plain}
 \chaptertoc
 …
 Note that expression \autoref{eq:DYN_hpg_sco} is commonly used when the variable volume formulation is activated
 (\texttt{vvl?}) because in that case, even with a flat bottom,
 the coordinate surfaces are not horizontal but follow the free surface \citep{levier.treguier.ea_rpt07}.
+the coordinate surfaces are not horizontal but follow the free surface \citep{levier.treguier.ea_trpt07}.
 The pressure jacobian scheme (\np[=.true.]{ln_dynhpg_prj}{ln\_dynhpg\_prj}) is available as
 an improved option to \np[=.true.]{ln_dynhpg_sco}{ln\_dynhpg\_sco} when \texttt{vvl?} is active.
 …
 which imposes a very small time step when an explicit time stepping is used.
 Two methods are proposed to allow a longer time step for the three-dimensional equations:
 the filtered free surface, which is a modification of the continuous equations (see \autoref{eq:MB_flt?}),
+the filtered free surface, which is a modification of the continuous equations \iffalse (see \autoref{eq:MB_flt?}) \fi
 and the split-explicit free surface described below.
 The extra term introduced in the filtered method is calculated implicitly,
 …
 external gravity waves in idealized or weakly non-linear cases.
 Although the damping is lower than for the filtered free surface,
 it is still significant as shown by \citet{levier.treguier.ea_rpt07} in the case of an analytical barotropic Kelvin wave.
+it is still significant as shown by \citet{levier.treguier.ea_trpt07} in the case of an analytical barotropic Kelvin wave.
 \cmtgm{               %%% copy from griffies Book
 …
 the atmospheric pressure is taken into account when computing the surface pressure gradient.
 (2) When \np[=.true.]{ln_tide_pot}{ln\_tide\_pot} and \np[=.true.]{ln_tide}{ln\_tide} (see \autoref{sec:SBC_tide}),
+(2) When \np[=.true.]{ln_tide_pot}{ln\_tide\_pot} and \np[=.true.]{ln_tide}{ln\_tide} (see \autoref{sec:SBC_TDE}),
 the tidal potential is taken into account when computing the surface pressure gradient.

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_LBC.tex

-                      r11693
+                      r14789
 \chapter{Lateral Boundary Condition (LBC)}
 \label{chap:LBC}
-\thispagestyle{plain}
 \chaptertoc
 …
     Release & Author(s) & Modifications \\
     \hline
+    {\em  next} & {\em Simon M{\" u}ller} & {\em Minor update of \autoref{subsec:LBC_bdy_tides}} \\[2mm]
     {\em   4.0} & {\em ...} & {\em ...} \\
     {\em   3.6} & {\em ...} & {\em ...} \\
 …
 %% =================================================================================================
 \section[Model domain boundary condition (\forcode{jperio})]{Model domain boundary condition (\protect\jp{jperio})}
+\section{Model domain boundary condition}
 \label{sec:LBC_jperio}
 …
 %% =================================================================================================
 \subsection[Closed, cyclic (\forcode{=0,1,2,7})]{Closed, cyclic (\protect\jp{jperio}\forcode{=0,1,2,7})}
+\subsection{Closed, cyclic (\forcode{l_Iperio,l_jperio})}
 \label{subsec:LBC_jperio012}
 The choice of closed or cyclic model domain boundary condition is made by
 setting \jp{jperio} to 0, 1, 2 or 7 in namelist \nam{cfg}{cfg}.
+setting \forcode{l_Iperio,l_jperio} to true or false in namelist \nam{cfg}{cfg}.
 Each time such a boundary condition is needed, it is set by a call to routine \mdl{lbclnk}.
 The computation of momentum and tracer trends proceeds from $i=2$ to $i=jpi-1$ and from $j=2$ to $j=jpj-1$,
 …
 \begin{description}
 \item [For closed boundary (\jp{jperio}\forcode{=0})], solid walls are imposed at all model boundaries:
+\item [For closed boundary (\forcode{l_Iperio = .false.,l_jperio = .false.})], solid walls are imposed at all model boundaries:
   first and last rows and columns are set to zero.
 \item [For cyclic east-west boundary (\jp{jperio}\forcode{=1})], first and last rows are set to zero (closed) whilst the first column is set to
+\item [For cyclic east-west boundary (\forcode{l_Iperio = .true.,l_jperio = .false.})], first and last rows are set to zero (closed) whilst the first column is set to
   the value of the last-but-one column and the last column to the value of the second one
   (\autoref{fig:LBC_jperio}-a).
   Whatever flows out of the eastern (western) end of the basin enters the western (eastern) end.
 \item [For cyclic north-south boundary (\jp{jperio}\forcode{=2})], first and last columns are set to zero (closed) whilst the first row is set to
+\item [For cyclic north-south boundary (\forcode{l_Iperio = .false.,l_jperio = .true.})], first and last columns are set to zero (closed) whilst the first row is set to
   the value of the last-but-one row and the last row to the value of the second one
   (\autoref{fig:LBC_jperio}-a).
   Whatever flows out of the northern (southern) end of the basin enters the southern (northern) end.
 \item [Bi-cyclic east-west and north-south boundary (\jp{jperio}\forcode{=7})] combines cases 1 and 2.
+\item [Bi-cyclic east-west and north-south boundary (\forcode{l_Iperio = .true.,l_jperio = .true.})] combines cases 1 and 2.
 \end{description}
 …
 %% =================================================================================================
 \subsection[North-fold (\forcode{=3,6})]{North-fold (\protect\jp{jperio}\forcode{=3,6})}
+\subsection{North-fold (\forcode{l_NFold = .true.})}
 \label{subsec:LBC_north_fold}
 …
   \includegraphics[width=0.66\textwidth]{LBC_North_Fold_T}
   \caption[North fold boundary in ORCA 2\deg, 1/4\deg and 1/12\deg]{
     North fold boundary with a $T$-point pivot and cyclic east-west boundary condition ($jperio=4$),
+    North fold boundary with a $T$-point pivot and cyclic east-west boundary condition ($c\_NFtype='T'$),
     as used in ORCA 2\deg, 1/4\deg and 1/12\deg.
     Pink shaded area corresponds to the inner domain mask (see text).}
 …
 Each processor is independent and without message passing or synchronous process, programs run alone and access just its own local memory.
 For this reason,
 the main model dimensions are now the local dimensions of the subdomain (pencil) that are named \jp{jpi}, \jp{jpj}, \jp{jpk}.
+the main model dimensions are now the local dimensions of the subdomain (pencil) that are named \texttt{jpi}, \texttt{jpj}, \texttt{jpk}.
 These dimensions include the internal domain and the overlapping rows.
 The number of rows to exchange (known as the halo) is usually set to one (nn\_hls=1, in \mdl{par\_oce},
+The number of rows to exchange (known as the halo) is usually set to one (\forcode{nn_hls=1}, in \mdl{par\_oce},
 and must be kept to one until further notice).
 The whole domain dimensions are named \jp{jpiglo}, \jp{jpjglo} and \jp{jpk}.
+The whole domain dimensions are named \texttt{jpiglo}, \texttt{jpjglo} and \texttt{jpk}.
 The relationship between the whole domain and a sub-domain is:
 \begin{gather*}
 …
 \end{gather*}
 One also defines variables nldi and nlei which correspond to the internal domain bounds, and the variables nimpp and njmpp which are the position of the (1,1) grid-point in the global domain (\autoref{fig:LBC_mpp}). Note that since the version 4, there is no more extra-halo area as defined in \autoref{fig:LBC_mpp} so \jp{jpi} is now always equal to nlci and \jp{jpj} equal to nlcj.
+One also defines variables nldi and nlei which correspond to the internal domain bounds, and the variables nimpp and njmpp which are the position of the (1,1) grid-point in the global domain (\autoref{fig:LBC_mpp}). Note that since the version 4, there is no more extra-halo area as defined in \autoref{fig:LBC_mpp} so \texttt{jpi} is now always equal to nlci and \texttt{jpj} equal to nlcj.
 An element of $T_{l}$, a local array (subdomain) corresponds to an element of $T_{g}$,
 …
 with $1 \leq i \leq jpi$, $1  \leq j \leq jpj $ , and  $1  \leq k \leq jpk$.
 The 1-d arrays $mig(1:\jp{jpi})$ and $mjg(1:\jp{jpj})$, defined in \rou{dom\_glo} routine (\mdl{domain} module), should be used to get global domain indices from local domain indices. The 1-d arrays, $mi0(1:\jp{jpiglo})$, $mi1(1:\jp{jpiglo})$ and $mj0(1:\jp{jpjglo})$, $mj1(1:\jp{jpjglo})$ have the reverse purpose and should be used to define loop indices expressed in global domain indices (see examples in \mdl{dtastd} module).\\
+The 1-d arrays $mig(1:\texttt{jpi})$ and $mjg(1:\texttt{jpj})$, defined in \rou{dom\_glo} routine (\mdl{domain} module), should be used to get global domain indices from local domain indices. The 1-d arrays, $mi0(1:\texttt{jpiglo})$, $mi1(1:\texttt{jpiglo})$ and $mj0(1:\texttt{jpjglo})$, $mj1(1:\texttt{jpjglo})$ have the reverse purpose and should be used to define loop indices expressed in global domain indices (see examples in \mdl{dtastd} module).\\
 The \NEMO\ model computes equation terms with the help of mask arrays (0 on land points and 1 on sea points). It is therefore possible that an MPI subdomain contains only land points. To save ressources, we try to supress from the computational domain as much land subdomains as possible. For example if $N_{mpi}$ processes are allocated to NEMO, the domain decomposition will be given by the following equation:
 …
 The BDY module was modelled on the OBC module (see \NEMO\ 3.4) and shares many features and
 a similar coding structure \citep{chanut_rpt05}.
+a similar coding structure \citep{chanut_trpt05}.
 The specification of the location of the open boundary is completely flexible and
 allows any type of setup, from regular boundaries to irregular contour (it includes the possibility to set an open boundary able to follow an isobath).
 …
 The number of boundary sets is defined by \np{nb_bdy}{nb\_bdy}.
 Each boundary set can be either defined as a series of straight line segments directly in the namelist
 (\np[=.false.]{ln_coords_file}{ln\_coords\_file}, and a namelist block \nam{bdy_index}{bdy\_index} must be included for each set) or read in from a file (\np[=.true.]{ln_coords_file}{ln\_coords\_file}, and a ``\ifile{coordinates.bdy}'' file must be provided).
 The coordinates.bdy file is analagous to the usual \NEMO\ ``\ifile{coordinates}'' file.
+(\np[=.false.]{ln_coords_file}{ln\_coords\_file}, and a namelist block \forcode{&nambdy_index} must be included for each set) or read in from a file (\np[=.true.]{ln_coords_file}{ln\_coords\_file}, and a ``\textit{coordinates.bdy.nc}'' file must be provided).
+The coordinates.bdy file is analagous to the usual \NEMO\ ``\textit{coordinates.nc}'' file.
 In the example above, there are two boundary sets, the first of which is defined via a file and
 the second is defined in the namelist.
 …
 \autoref{fig:LBC_bdy_geom} shows an example of an irregular boundary.
 The boundary geometry for each set may be defined in a namelist nambdy\_index or
 by reading in a ``\ifile{coordinates.bdy}'' file.
 The nambdy\_index namelist defines a series of straight-line segments for north, east, south and west boundaries.
 One nambdy\_index namelist block is needed for each boundary condition defined by indexes.
+The boundary geometry for each set may be defined in a namelist \forcode{&nambdy_index} or
+by reading in a ``\textit{coordinates.bdy.nc}'' file.
+The \forcode{&nambdy_index} namelist defines a series of straight-line segments for north, east, south and west boundaries.
+One \forcode{&nambdy_index} namelist block is needed for each boundary condition defined by indexes.
 For the northern boundary, \texttt{nbdysegn} gives the number of segments,
 \jp{jpjnob} gives the $j$ index for each segment and \jp{jpindt} and
 \jp{jpinft} give the start and end $i$ indices for each segment with similar for the other boundaries.
+\texttt{jpjnob} gives the $j$ index for each segment and \texttt{jpindt} and
+\texttt{jpinft} give the start and end $i$ indices for each segment with similar for the other boundaries.
 These segments define a list of $T$ grid points along the outermost row of the boundary ($nbr\,=\, 1$).
 The code deduces the $U$ and $V$ points and also the points for $nbr\,>\, 1$ if \np[>1]{nn_rimwidth}{nn\_rimwidth}.
 The boundary geometry may also be defined from a ``\ifile{coordinates.bdy}'' file.
+The boundary geometry may also be defined from a ``\textit{coordinates.bdy.nc}'' file.
 \autoref{fig:LBC_nc_header} gives an example of the header information from such a file, based on the description of geometrical setup given above.
 The file should contain the index arrays for each of the $T$, $U$ and $V$ grids.
 …
   \centering
   \includegraphics[width=0.66\textwidth]{LBC_nc_header}
   \caption[Header for a \protect\ifile{coordinates.bdy} file]{
     Example of the header for a \protect\ifile{coordinates.bdy} file}
+  \caption[Header for a \textit{coordinates.bdy.nc} file]{
+    Example of the header for a \textit{coordinates.bdy.nc} file}
   \label{fig:LBC_nc_header}
 \end{figure}
 …
 Tidal forcing at open boundaries requires the activation of surface
+tides (i.e., in \nam{_tide}{\_tide}, \np{ln_tide}{ln\_tide} needs to be set to
+\forcode{.true.} and the required constituents need to be activated by
+including their names in the \np{clname}{clname} array; see
+\autoref{sec:SBC_tide}). Specific options related to the reading in of
+tides (i.e., in \nam{_tide}{\_tide}, \np[=.true.]{ln_tide}{ln\_tide} with the active tidal
+constituents listed in the \np{sn_tide_cnames}{sn\_tide\_cnames} array; see
+\autoref{sec:SBC_TDE}). The specific options related to the reading in of
 the complex harmonic amplitudes of elevation (SSH) and barotropic
 velocity (u,v) at open boundaries are defined through the
 \nam{bdy_tide}{bdy\_tide} namelist parameters.\\
+velocity components (u,v) at the open boundaries are defined through the
+\nam{bdy_tide}{bdy\_tide} namelist parameters.\par
 The tidal harmonic data at open boundaries can be specified in two
 different ways, either on a two-dimensional grid covering the entire
 model domain or along open boundary segments; these two variants can
+be selected by setting \np{ln_bdytide_2ddta }{ln\_bdytide\_2ddta } to \forcode{.true.} or
+\forcode{.false.}, respectively. In either case, the real and
+imaginary parts of SSH and the two barotropic velocity components for
+each activated tidal constituent \textit{tcname} have to be provided
+separately: when two-dimensional data is used, variables
+\textit{tcname\_z1} and \textit{tcname\_z2} for real and imaginary SSH,
+respectively, are expected in input file \np{filtide}{filtide} with suffix
+\ifile{\_grid\_T}, variables \textit{tcname\_u1} and
+\textit{tcname\_u2} for real and imaginary u, respectively, are
+expected in input file \np{filtide}{filtide} with suffix \ifile{\_grid\_U}, and
+\textit{tcname\_v1} and \textit{tcname\_v2} for real and imaginary v,
+respectively, are expected in input file \np{filtide}{filtide} with suffix
+\ifile{\_grid\_V}; when data along open boundary segments is used,
+variables \textit{z1} and \textit{z2} (real and imaginary part of SSH)
+are expected to be available from file \np{filtide}{filtide} with suffix
+\ifile{tcname\_grid\_T}, variables \textit{u1} and \textit{u2} (real
+and imaginary part of u) are expected to be available from file
+\np{filtide}{filtide} with suffix \ifile{tcname\_grid\_U}, and variables
+\textit{v1} and \textit{v2} (real and imaginary part of v) are
+expected to be available from file \np{filtide}{filtide} with suffix
+\ifile{tcname\_grid\_V}. If \np{ln_bdytide_conj}{ln\_bdytide\_conj} is set to
+\forcode{.true.}, the data is expected to be in complex conjugate
+form.
+be selected by setting \np[=.true.]{ln_bdytide_2ddta}{ln\_bdytide\_2ddta} or
+\np[=.false.]{ln_bdytide_2ddta}{ln\_bdytide\_2ddta}, respectively. In either
+case, the real and imaginary parts of SSH, u, and v amplitudes associated with
+each activated tidal constituent \texttt{<constituent>} have to be provided
+separately as fields in input files with names based on
+\np[=<input>]{filtide}{filtide}: when two-dimensional data is used, variables
+\texttt{<constituent>\_z1} and \texttt{<constituent>\_z2} for the real and imaginary parts of
+SSH, respectively, are expected to be available in file
+\textit{<input>\_grid\_T.nc}, variables \texttt{<constituent>\_u1} and
+\texttt{<constituent>\_u2} for the real and imaginary parts of u, respectively, in file
+\textit{<input>\_grid\_U.nc}, and \texttt{<constituent>\_v1} and
+\texttt{<constituent>\_v2} for the real and imaginary parts of v, respectively, in file
+\textit{<input>\_grid\_V.nc}; when data along open boundary segments is used,
+variables \texttt{z1} and \texttt{z2} (real and imaginary part of SSH) are
+expected to be available in file \textit{<input><constituent>\_grid\_T.nc},
+variables \texttt{u1} and \texttt{u2} (real and imaginary part of u) in file
+\textit{<input><constituent>\_grid\_U.nc}, and variables \texttt{v1} and \texttt{v2}
+(real and imaginary part of v) in file
+\textit{<input><constituent>\_grid\_V.nc}.\par
 Note that the barotropic velocity components are assumed to be defined

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_LDF.tex

-                      r11693
+                      r14789
 \chapter{Lateral Ocean Physics (LDF)}
 \label{chap:LDF}
-\thispagestyle{plain}
 \chaptertoc
 …
 \subsection[Deformation rate dependent viscosities (\forcode{nn_ahm_ijk_t=32})]{Deformation rate dependent viscosities (\protect\np[=32]{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t})}
 This option refers to the \citep{smagorinsky_MW63} scheme which is here implemented for momentum only. Smagorinsky chose as a
+This option refers to the \citep{smagorinsky_MWR63} scheme which is here implemented for momentum only. Smagorinsky chose as a
 characteristic time scale $T_{smag}$ the deformation rate and for the lengthscale $L_{smag}$ the maximum wavenumber possible on the horizontal grid, e.g.:
 …
 \end{listing}
 If  \np[=.true.]{ln_mle}{ln\_mle} in \nam{tra_mle}{tra\_mle} namelist, a parameterization of the mixing due to unresolved mixed layer instabilities is activated (\citet{foxkemper.ferrari_JPO08}). Additional transport is computed in \rou{ldf\_mle\_trp} and added to the eulerian transport in \rou{tra\_adv} as done for eddy induced advection.
+If  \np[=.true.]{ln_mle}{ln\_mle} in \nam{tra_mle}{tra\_mle} namelist, a parameterization of the mixing due to unresolved mixed layer instabilities is activated (\citet{fox-kemper.ferrari.ea_JPO08}). Additional transport is computed in \rou{ldf\_mle\_trp} and added to the eulerian transport in \rou{tra\_adv} as done for eddy induced advection.
 \colorbox{yellow}{TBC}

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_OBS.tex

-                      r11708
+                      r14789
 %    {\em --\texttt{"}--} & {\em ... K. Mogensen, A. Vidard, A. Weaver} & {\em ---\texttt{"}---}  \\
 %\end{tabular}
-\thispagestyle{plain}
 \chaptertoc
 …
 To use Sea Level Anomaly (SLA) data the mean dynamic topography (MDT) must be provided in a separate file defined on
 the model grid called \ifile{slaReferenceLevel}.
+the model grid called \textit{slaReferenceLevel.nc}.
 The MDT is required in order to produce the model equivalent sea level anomaly from the model sea surface height.
 Below is an example header for this file (on the ORCA025 grid).
 …
 \subsubsection{Running}
 The simplest way to use the executable is to edit and append the \textbf{sao.nml} namelist to
+The simplest way to use the executable is to edit and append the \nam{sao}{sao} namelist to
 a full \NEMO\ namelist and then to run the executable as if it were nemo.exe.
 …
 For example, to read the second time counter from a single file the namelist would be.
+\begin{forlines}
+\begin{listing}
+  \begin{forlines}
 !----------------------------------------------------------------------
 !       namsao Standalone obs_oper namelist
 …
    nn_sao_idx = 2
+/
+\end{forlines}
+  \end{forlines}
+  \caption{\forcode{&namsao}}
+  \label{lst:namsao}
+\end{listing}
 %% =================================================================================================
 …
 To plot some data run IDL and then:
 \begin{minted}{idl}
+\begin{verbatim}
 IDL> dataplot, "filename"
 \end{minted}
+\end{verbatim}
 To read multiple files into dataplot,
 …
 the easiest method is to use the spawn command to generate a list of files which can then be passed to dataplot.
 \begin{minted}{idl}
+\begin{verbatim}
 IDL> spawn, 'ls profb*.nc', files
 IDL> dataplot, files
 \end{minted}
+\end{verbatim}
 \autoref{fig:OBS_dataplotmain} shows the main window which is launched when dataplot starts.

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_SBC.tex

-                      r13165
+                      r14789
 \documentclass[../main/NEMO_manual]{subfiles}
-\usepackage{fontspec}
-\usepackage{fontawesome}
 \begin{document}
 \chapter{Surface Boundary Condition (SBC, SAS, ISF, ICB)}
+\chapter{Surface Boundary Condition (SBC, SAS, ISF, ICB, TDE)}
 \label{chap:SBC}
-\thispagestyle{plain}
 \chaptertoc
 …
     Release & Author(s) & Modifications \\
     \hline
+    {\em  next} & {\em Simon M{\" u}ller} & {\em Update of \autoref{sec:SBC_TDE}; revision of \autoref{subsec:SBC_fwb}}\\[2mm]
+    {\em  next} & {\em Pierre Mathiot} & {\em update of the ice shelf section (2019 developments)}\\[2mm]
     {\em   4.0} & {\em ...} & {\em ...} \\
     {\em   3.6} & {\em ...} & {\em ...} \\
 …
   (\np[=0..3]{nn_ice}{nn\_ice}),
 \item the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np[=.true.]{ln_rnf}{ln\_rnf}),
-\item the addition of ice-shelf melting as lateral inflow (parameterisation) or
-  as fluxes applied at the land-ice ocean interface (\np[=.true.]{ln_isf}{ln\_isf}),
 \item the addition of a freshwater flux adjustment in order to avoid a mean sea-level drift
   (\np[=0..2]{nn_fwb}{nn\_fwb}),
 …
 One of these is modification by icebergs (see \autoref{sec:SBC_ICB_icebergs}),
 which act as drifting sources of fresh water.
-Another example of modification is that due to the ice shelf melting/freezing (see \autoref{sec:SBC_isf}),
-which provides additional sources of fresh water.
 %% =================================================================================================
 …
 See \autoref{subsec:SBC_ssr} for its specification.
+%% =================================================================================================
+\pagebreak
+\newpage
+%% =================================================================================================
 \section[Bulk formulation (\textit{sbcblk.F90})]{Bulk formulation (\protect\mdl{sbcblk})}
 \label{sec:SBC_blk}
 …
 Note: all the NEMO Fortran routines involved in the present section have been
  initially developed (and are still developed in parallel) in
  the \href{https://brodeau.github.io/aerobulk/}{\texttt{AeroBulk}} open-source project
 \citep{brodeau.barnier.ea_JPO17}.
+initially developed (and are still developed in parallel) in
+the \href{https://brodeau.github.io/aerobulk}{\texttt{AeroBulk}} open-source project
+\citep{brodeau.barnier.ea_JPO16}.
 %%% Bulk formulae are this:
+\subsection{Bulk formulae}\label{subsec:SBC_blkform}
+%
+\subsection{Bulk formulae}
+\label{subsec:SBC_blkform}
 In NEMO, the set of equations that relate each component of the surface fluxes
 to the near-surface atmosphere and sea surface states writes
+%
+\begin{subequations}\label{eq_bulk}
+\begin{subequations}
+  \label{eq:SBC_bulk}
   \label{eq:SBC_bulk_form}
+  \begin{eqnarray}
+    \mathbf{\tau} &=& \rho~ C_D ~ \mathbf{U}_z  ~ U_B \\
+    Q_H           &=& \rho~C_H~C_P~\big[ \theta_z - T_s \big] ~ U_B \\
+    E             &=& \rho~C_E    ~\big[    q_s   - q_z \big] ~ U_B \\
+    Q_L           &=& -L_v \, E \\
+    %
+    Q_{sr}        &=& (1 - a) Q_{sw\downarrow} \\
+    Q_{ir}        &=& \delta (Q_{lw\downarrow} -\sigma T_s^4)
+  \end{eqnarray}
+  \begin{align}
+    \mathbf{\tau} &= \rho~ C_D ~ \mathbf{U}_z  ~ U_B \\
+    Q_H           &= \rho~C_H~C_P~\big[ \theta_z - T_s \big] ~ U_B \\
+    E             &= \rho~C_E    ~\big[    q_s   - q_z \big] ~ U_B \\
+    Q_L           &= -L_v \, E \\
+    Q_{sr}        &= (1 - a) Q_{sw\downarrow} \\
+    Q_{ir}        &= \delta (Q_{lw\downarrow} -\sigma T_s^4)
+  \end{align}
 \end{subequations}
+%
 with
    \[ \theta_z \simeq T_z+\gamma z \]
    \[  q_s \simeq 0.98\,q_{sat}(T_s,p_a ) \]
+%
 from which, the the non-solar heat flux is \[ Q_{ns} = Q_L + Q_H + Q_{ir} \]
+%
 where $\mathbf{\tau}$ is the wind stress vector, $Q_H$ the sensible heat flux,
 $E$ the evaporation, $Q_L$ the latent heat flux, and $Q_{ir}$ the net longwave
 flux.
+%
 $Q_{sw\downarrow}$ and $Q_{lw\downarrow}$ are the surface downwelling shortwave
 and longwave radiative fluxes, respectively.
+%
 Note: a positive sign for $\mathbf{\tau}$, $Q_H$, $Q_L$, $Q_{sr}$ or $Q_{ir}$
 implies a gain of the relevant quantity for the ocean, while a positive $E$
 implies a freshwater loss for the ocean.
+%
 $\rho$ is the density of air. $C_D$, $C_H$ and $C_E$ are the bulk transfer
 coefficients for momentum, sensible heat, and moisture, respectively.
+%
 $C_P$ is the heat capacity of moist air, and $L_v$ is the latent heat of
 vaporization of water.
+%
 $\theta_z$, $T_z$ and $q_z$ are the potential temperature, absolute temperature,
 and specific humidity of air at height $z$ above the sea surface,
 respectively. $\gamma z$ is a temperature correction term which accounts for the
 adiabatic lapse rate and approximates the potential temperature at height
+$z$ \citep{josey.gulev.ea_2013}.
+%
+$z$ \citep{josey.gulev.ea_OCC13}.
 $\mathbf{U}_z$ is the wind speed vector at height $z$ above the sea surface
+(possibly referenced to the surface current $\mathbf{u_0}$,
+section \ref{s_res1}.\ref{ss_current}).
+%
+(possibly referenced to the surface current $\mathbf{u_0}$).%,
+%\autoref{s_res1}.\autoref{ss_current}). %% Undefined references
 The bulk scalar wind speed, namely $U_B$, is the scalar wind speed,
 $|\mathbf{U}_z|$, with the potential inclusion of a gustiness contribution.
+%
 $a$ and $\delta$ are the albedo and emissivity of the sea surface, respectively.\\
+%
 %$p_a$ is the mean sea-level pressure (SLP).
+%
 $T_s$ is the sea surface temperature. $q_s$ is the saturation specific humidity
 of air at temperature $T_s$; it includes a 2\% reduction to account for the
 presence of salt in seawater \citep{sverdrup.johnson.ea_1942,kraus.businger_QJRMS96}.
+presence of salt in seawater \citep{sverdrup.johnson.ea_bk42,kraus.businger_QJRMS96}.
 Depending on the bulk parametrization used, $T_s$ can either be the temperature
 at the air-sea interface (skin temperature, hereafter SSST) or at typically a
 few tens of centimeters below the surface (bulk sea surface temperature,
 hereafter SST).
+%
 The SSST differs from the SST due to the contributions of two effects of
 opposite sign, the \emph{cool skin} and \emph{warm layer} (hereafter CS and WL,
+respectively, see section\,\ref{subsec:SBC_skin}).
+%
+respectively, see \autoref{subsec:SBC_skin}).
 Technically, when the ECMWF or COARE* bulk parametrizations are selected
 (\np[=.true.]{ln_ECMWF}{ln\_ECMWF} or \np[=.true.]{ln_COARE*}{ln\_COARE\*}),
 …
 For more details on all these aspects the reader is invited to refer
+to \citet{brodeau.barnier.ea_JPO17}.
+\subsection{Bulk parametrizations}\label{subsec:SBC_blk_ocean}
+to \citet{brodeau.barnier.ea_JPO16}.
+\subsection{Bulk parametrizations}
+\label{subsec:SBC_blk_ocean}
 %%%\label{subsec:SBC_param}
 …
 height (from \np{rn_zqt}{rn\_zqt} to \np{rn_zu}{rn\_zu}).
 For the open ocean, four bulk parametrization algorithms are available in NEMO:
 \begin{itemize}
 \item NCAR, formerly known as CORE, \citep{large.yeager_rpt04,large.yeager_CD09}
+\item NCAR, formerly known as CORE, \citep{large.yeager_trpt04,large.yeager_CD09}
 \item COARE 3.0 \citep{fairall.bradley.ea_JC03}
 \item COARE 3.6 \citep{edson.jampana.ea_JPO13}
 …
 \end{itemize}
 With respect to version 3, the principal advances in version 3.6 of the COARE
 bulk parametrization are built around improvements in the representation of the
 effects of waves on
 fluxes \citep{edson.jampana.ea_JPO13,brodeau.barnier.ea_JPO17}. This includes
+fluxes \citep{edson.jampana.ea_JPO13,brodeau.barnier.ea_JPO16}. This includes
 improved relationships of surface roughness, and whitecap fraction on wave
 parameters. It is therefore recommended to chose version 3.6 over 3.
+\subsection{Cool-skin and warm-layer parametrizations}\label{subsec:SBC_skin}
+%\subsection[Cool-skin and warm-layer parameterizations
+%(\forcode{ln_skin_cs} \& \forcode{ln_skin_wl})]{Cool-skin and warm-layer parameterizations (\protect\np{ln_skin_cs}{ln\_skin\_cs} \& \np{ln_skin_wl}{ln\_skin\_wl})}
+%\label{subsec:SBC_skin}
+%
+\subsection[Cool-skin and warm-layer parameterizations (   \forcode{ln_skin_cs}               \& \forcode{ln_skin_wl}              )]
+           {Cool-skin and warm-layer parameterizations (\protect\np{ln_skin_cs}{ln\_skin\_cs} \&      \np{ln_skin_wl}{ln\_skin\_wl})}
+\label{subsec:SBC_skin}
 As opposed to the NCAR bulk parametrization, more advanced bulk
 parametrizations such as COARE3.x and ECMWF are meant to be used with the skin
 temperature $T_s$ rather than the bulk SST (which, in NEMO is the temperature at
 the first T-point level, see section\,\ref{subsec:SBC_blkform}).
+%
+the first T-point level, see \autoref{subsec:SBC_blkform}).
 As such, the relevant cool-skin and warm-layer parametrization must be
 activated through \np[=T]{ln_skin_cs}{ln\_skin\_cs}
 …
 For the cool-skin scheme parametrization COARE and ECMWF algorithms share the same
 basis: \citet{fairall.bradley.ea_JGR96}. With some minor updates based
 on \citet{zeng.beljaars_GRL05} for ECMWF, and \citet{fairall.ea_19} for COARE
+basis: \citet{fairall.bradley.ea_JGRO96}. With some minor updates based
+on \citet{zeng.beljaars_GRL05} for ECMWF \iffalse, and \citet{fairall.ea_19?} for COARE \fi
 .6.
 …
 turbulence input from Langmuir circulation).
 Importantly, COARE warm-layer scheme \citep{fairall.ea_19} includes a prognostic
+Importantly, COARE warm-layer scheme \iffalse \citep{fairall.ea_19?} \fi includes a prognostic
 equation for the thickness of the warm-layer, while it is considered as constant
 in the ECWMF algorithm.
 \subsection{Appropriate use of each bulk parametrization}
 …
 temperature is the bulk SST. Hence the following namelist parameters must be
 set:
+%
 \begin{verbatim}
+\begin{forlines}
   ...
   ln_NCAR    = .true.
 …
   ...
   ln_humi_sph = .true. ! humidity "sn_humi" is specific humidity  [kg/kg]
+\end{verbatim}
+\end{forlines}
 \subsubsection{ECMWF}
+%
 With an atmospheric forcing based on a reanalysis of the ECMWF, such as the
 Drakkar Forcing Set \citep{brodeau.barnier.ea_OM10}, we strongly recommend to
 …
 humidity are provided at the 2\,m height, and given that the humidity is
 distributed as the dew-point temperature, the namelist must be tuned as follows:
+%
 \begin{verbatim}
+\begin{forlines}
   ...
   ln_ECMWF   = .true.
 …
   ln_humi_dpt = .true. !  humidity "sn_humi" is dew-point temperature [K]
   ...
 \end{verbatim}
+%
+\end{forlines}
 Note: when \np{ln_ECMWF}{ln\_ECMWF} is selected, the selection
 of \np{ln_skin_cs}{ln\_skin\_cs} and \np{ln_skin_wl}{ln\_skin\_wl} implicitly
 …
 respectively (found in \textit{sbcblk\_skin\_ecmwf.F90}).
 \subsubsection{COARE 3.x}
+%
 Since the ECMWF parametrization is largely based on the COARE* parametrization,
 the two algorithms are very similar in terms of structure and closure
 approach. As such, the namelist tuning for COARE 3.x is identical to that of
 ECMWF:
+%
 \begin{verbatim}
+\begin{forlines}
   ...
   ln_COARE3p6 = .true.
 …
   ln_skin_wl = .true. ! use the warm-layer parameterization
   ...
 \end{verbatim}
+\end{forlines}
 Note: when \np[=T]{ln_COARE3p0}{ln\_COARE3p0} is selected, the selection
 …
 respectively (found in \textit{sbcblk\_skin\_coare.F90}).
 %lulu
 % In a typical bulk algorithm, the BTCs under neutral stability conditions are
 …
 % and $q_z$.
 \subsection{Prescribed near-surface atmospheric state}
 …
 different bulk formulae are used for the turbulent fluxes computation over the
 ocean and over sea-ice surface.
+%
 %The choice is made by setting to true one of the following namelist
 …
 the namsbc\_blk namelist (see \autoref{subsec:SBC_fldread}).
 \subsubsection{Air humidity}
 …
 [kg/kg], relative humidity [\%], or dew-point temperature [K] (LINK to namelist
 parameters)...
-~\\
 %% =================================================================================================
 …
 %their neutral transfer coefficients relationships with neutral wind.
 %\begin{itemize}
 %\item NCAR (\np[=.true.]{ln_NCAR}{ln\_NCAR}): The NCAR bulk formulae have been developed by \citet{large.yeager_rpt04}.
+%\item NCAR (\np[=.true.]{ln_NCAR}{ln\_NCAR}): The NCAR bulk formulae have been developed by \citet{large.yeager_trpt04}.
 %  They have been designed to handle the NCAR forcing, a mixture of NCEP reanalysis and satellite data.
 %  They use an inertial dissipative method to compute the turbulent transfer coefficients
 %  (momentum, sensible heat and evaporation) from the 10m wind speed, air temperature and specific humidity.
 %  This \citet{large.yeager_rpt04} dataset is available through
+%  This \citet{large.yeager_trpt04} dataset is available through
 %  the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/NCAR.html}{GFDL web site}.
 %  Note that substituting ERA40 to NCEP reanalysis fields does not require changes in the bulk formulea themself.
 …
 \label{subsec:SBC_blk_ice}
 \texttt{\#out\_of\_place:}
  For sea-ice, three possibilities can be selected:
 a constant transfer coefficient (1.4e-3; default
 value), \citet{lupkes.gryanik.ea_JGR12} (\np{ln_Cd_L12}{ln\_Cd\_L12}),
+value), \citet{lupkes.gryanik.ea_JGRA12} (\np{ln_Cd_L12}{ln\_Cd\_L12}),
 and \citet{lupkes.gryanik_JGR15} (\np{ln_Cd_L15}{ln\_Cd\_L15}) parameterizations
 \texttt{\#out\_of\_place.}
 Surface turbulent fluxes between sea-ice and the atmosphere can be computed in three different ways:
 \begin{itemize}
 \item Constant value (\np[ Cd_ice=1.4e-3 ]{constant value}{constant\ value}):
+\item Constant value (\forcode{Cd_ice=1.4e-3}):
   default constant value used for momentum and heat neutral transfer coefficients
 \item \citet{lupkes.gryanik.ea_JGR12} (\np[=.true.]{ln_Cd_L12}{ln\_Cd\_L12}):
+\item \citet{lupkes.gryanik.ea_JGRA12} (\np[=.true.]{ln_Cd_L12}{ln\_Cd\_L12}):
   This scheme adds a dependency on edges at leads, melt ponds and flows
   of the constant neutral air-ice drag. After some approximations,
 …
 %% =================================================================================================
 \section[Surface tides (\textit{sbctide.F90})]{Surface tides (\protect\mdl{sbctide})}
 \label{sec:SBC_tide}
+\section{Surface tides (TDE)}
+\label{sec:SBC_TDE}
 \begin{listing}
 …
 \end{listing}
+The tidal forcing, generated by the gravity forces of the Earth-Moon and Earth-Sun sytems,
+is activated if \np{ln_tide}{ln\_tide} and \np{ln_tide_pot}{ln\_tide\_pot} are both set to \forcode{.true.} in \nam{_tide}{\_tide}.
+This translates as an additional barotropic force in the momentum \autoref{eq:MB_PE_dyn} such that:
+\subsection{Tidal constituents}
+Ocean model component TDE provides the common functionality for tidal forcing
+and tidal analysis in the model framework. This includes the computation of the gravitational
+surface forcing, as well as support for lateral forcing at open boundaries (see
+\autoref{subsec:LBC_bdy_tides}) and tidal harmonic analysis \iffalse (see
+\autoref{subsec:DIA_diamlr?} and \autoref{subsec:DIA_diadetide?}) \fi . The module is
+activated with \np[=.true.]{ln_tide}{ln\_tide} in namelist
+\nam{_tide}{\_tide}. It provides the same 34 tidal constituents that are
+included in the
+\href{https://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes.html}{FES2014
+  ocean tide model}: Mf, Mm, Ssa, Mtm, Msf, Msqm, Sa, K1, O1, P1, Q1, J1, S1,
+M2, S2, N2, K2, nu2, mu2, 2N2, L2, T2, eps2, lam2, R2, M3, MKS2, MN4, MS4, M4,
+N4, S4, M6, and M8; see file \textit{tide.h90} and \mdl{tide\_mod} for further
+information and references\footnote{As a legacy option \np{ln_tide_var}{ln\_tide\_var} can be
+  set to \forcode{0}, in which case the 19 tidal constituents (M2, N2, 2N2, S2,
+  K2, K1, O1, Q1, P1, M4, Mf, Mm, Msqm, Mtm, S1, MU2, NU2, L2, and T2; see file
+  \textit{tide.h90}) and associated parameters that have been available in NEMO version
+.0 and earlier are available}. Constituents to be included in the tidal forcing
+(surface and lateral boundaries) are selected by enumerating their respective
+names in namelist array \np{sn_tide_cnames}{sn\_tide\_cnames}.\par
+\subsection{Surface tidal forcing}
+Surface tidal forcing can be represented in the model through an additional
+barotropic force in the momentum equation (\autoref{eq:MB_PE_dyn}) such that:
 \[
+  % \label{eq:SBC_PE_dyn_tides}
+  \frac{\partial {\mathrm {\mathbf U}}_h }{\partial t}= ...
+  +g\nabla (\Pi_{eq} + \Pi_{sal})
+  \frac{\partial {\mathrm {\mathbf U}}_h }{\partial t} = \ldots +g\nabla (\gamma
+  \Pi_{eq} + \Pi_{sal})
 \]
+where $\Pi_{eq}$ stands for the equilibrium tidal forcing and
+$\Pi_{sal}$ is a self-attraction and loading term (SAL).
+The equilibrium tidal forcing is expressed as a sum over a subset of
+constituents chosen from the set of available tidal constituents
+defined in file \hf{SBC/tide} (this comprises the tidal
+constituents \textit{M2, N2, 2N2, S2, K2, K1, O1, Q1, P1, M4, Mf, Mm,
+  Msqm, Mtm, S1, MU2, NU2, L2}, and \textit{T2}). Individual
+constituents are selected by including their names in the array
+\np{clname}{clname} in \nam{_tide}{\_tide} (e.g., \np{clname}{clname}\forcode{(1)='M2', }
+\np{clname}{clname}\forcode{(2)='S2'} to select solely the tidal consituents \textit{M2}
+and \textit{S2}). Optionally, when \np{ln_tide_ramp}{ln\_tide\_ramp} is set to
+\forcode{.true.}, the equilibrium tidal forcing can be ramped up
+linearly from zero during the initial \np{rdttideramp}{rdttideramp} days of the
+model run.
+where $\gamma \Pi_{eq}$ stands for the equilibrium tidal forcing scaled by a spatially
+uniform tilt factor $\gamma$, and $\Pi_{sal}$ is an optional
+self-attraction and loading term (SAL). These additional terms are enabled when,
+in addition to \np[=.true.]{ln_tide}{ln\_tide}),
+\np[=.true.]{ln_tide_pot}{ln\_tide\_pot}.\par
+The equilibrium tidal forcing is expressed as a sum over the subset of
+constituents listed in \np{sn_tide_cnames}{sn\_tide\_cnames} of
+\nam{_tide} (e.g.,
+\begin{forlines}
+      sn_tide_cnames(1) = 'M2'
+      sn_tide_cnames(2) = 'K1'
+      sn_tide_cnames(3) = 'S2'
+      sn_tide_cnames(4) = 'O1'
+\end{forlines}
+to select the four tidal constituents of strongest equilibrium tidal
+potential). The tidal tilt factor $\gamma = 1 + k - h$ includes the
+Love numbers $k$ and $h$ \citep{love_PRSL09}; this factor is
+configurable using \np{rn_tide_gamma}{rn\_tide\_gamma} (default value 0.7). Optionally,
+when \np[=.true.]{ln_tide_ramp}{ln\_tide\_ramp}, the equilibrium tidal
+forcing can be ramped up linearly from zero during the initial
+\np{rn_tide_ramp_dt}{rn\_tide\_ramp\_dt} days of the model run.\par
 The SAL term should in principle be computed online as it depends on
 the model tidal prediction itself (see \citet{arbic.garner.ea_DSR04} for a
+discussion about the practical implementation of this term).
+Nevertheless, the complex calculations involved would make this
+computationally too expensive. Here, two options are available:
+$\Pi_{sal}$ generated by an external model can be read in
+(\np[=.true.]{ln_read_load}{ln\_read\_load}), or a ``scalar approximation'' can be
+used (\np[=.true.]{ln_scal_load}{ln\_scal\_load}). In the latter case
+discussion about the practical implementation of this term). The complex
+calculations involved in such computations, however, are computationally very
+expensive. Here, two mutually exclusive simpler variants are available:
+amplitudes generated by an external model for oscillatory $\Pi_{sal}$
+contributions from each of the selected tidal constituents can be read in
+(\np[=.true.]{ln_read_load}{ln\_read\_load}) from the file specified in
+\np{cn_tide_load}{cn\_tide\_load} (the variable names are comprised of the
+tidal-constituent name and suffixes \forcode{_z1} and \forcode{_z2} for the two
+orthogonal components, respectively); alternatively, a ``scalar approximation''
+can be used (\np[=.true.]{ln_scal_load}{ln\_scal\_load}), where
 \[
   \Pi_{sal} = \beta \eta,
 \]
+where $\beta$ (\np{rn_scal_load}{rn\_scal\_load} with a default value of 0.094) is a
+spatially constant scalar, often chosen to minimize tidal prediction
+errors. Setting both \np{ln_read_load}{ln\_read\_load} and \np{ln_scal_load}{ln\_scal\_load} to
+\forcode{.false.} removes the SAL contribution.
+with a spatially uniform coefficient $\beta$, which can be configured
+via \np{rn_scal_load}{rn\_scal\_load} (default value 0.094) and is
+often tuned to minimize tidal prediction errors.\par
+For diagnostic purposes, the forcing potential of the individual tidal
+constituents (incl. load ptential, if activated) and the total forcing
+potential (incl. load potential, if activated) can be made available
+as diagnostic output by setting
+\np[=.true.]{ln_tide_dia}{ln\_tide\_dia} (fields
+\forcode{tide_pot_<constituent>} and \forcode{tide_pot}).\par
 %% =================================================================================================
 …
 %% =================================================================================================
 \section[Ice shelf melting (\textit{sbcisf.F90})]{Ice shelf melting (\protect\mdl{sbcisf})}
+\section[Ice Shelf (ISF)]{Interaction with ice shelves (ISF)}
 \label{sec:SBC_isf}
 \begin{listing}
   \nlst{namsbc_isf}
   \caption{\forcode{&namsbc_isf}}
   \label{lst:namsbc_isf}
+  \nlst{namisf}
+  \caption{\forcode{&namisf}}
+  \label{lst:namisf}
 \end{listing}
+The namelist variable in \nam{sbc}{sbc}, \np{nn_isf}{nn\_isf}, controls the ice shelf representation.
+Description and result of sensitivity test to \np{nn_isf}{nn\_isf} are presented in \citet{mathiot.jenkins.ea_GMD17}.
+The different options are illustrated in \autoref{fig:SBC_isf}.
+The namelist variable in \nam{isf}{isf}, \np{ln_isf}{ln\_isf}, controls the ice shelf interactions:
 \begin{description}
+  \item [{\np[=1]{nn_isf}{nn\_isf}}]: The ice shelf cavity is represented (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed).
+  The fwf and heat flux are depending of the local water properties.
+  Two different bulk formulae are available:
+   \item $\bullet$ representation of the ice shelf/ocean melting/freezing for opened cavity (cav, \np{ln_isfcav_mlt}{ln\_isfcav\_mlt}).
+   \item $\bullet$ parametrisation of the ice shelf/ocean melting/freezing for closed cavities (par, \np{ln_isfpar_mlt}{ln\_isfpar\_mlt}).
+   \item $\bullet$ coupling with an ice sheet model (\np{ln_isfcpl}{ln\_isfcpl}).
+\end{description}
+  \subsection{Ocean/Ice shelf fluxes in opened cavities}
+     \np{ln_isfcav_mlt}{ln\_isfcav\_mlt}\forcode{ = .true.} activates the ocean/ice shelf thermodynamics interactions at the ice shelf/ocean interface.
+     If \np{ln_isfcav_mlt}{ln\_isfcav\_mlt}\forcode{ = .false.}, thermodynamics interactions are desctivated but the ocean dynamics inside the cavity is still active.
+     The logical flag \np{ln_isfcav}{ln\_isfcav} control whether or not the ice shelf cavities are closed. \np{ln_isfcav}{ln\_isfcav} is not defined in the namelist but in the domcfg.nc input file.\\
+options are available to represent to ice-shelf/ocean fluxes at the interface:
+     \begin{description}
+        \item[\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = 'spe'}]:
+        The fresh water flux is specified by a forcing fields \np{sn_isfcav_fwf}{sn\_isfcav\_fwf}. Convention of the input file is: positive toward the ocean (i.e. positive for melting and negative for freezing).
+        The latent heat fluxes is derived from the fresh water flux.
+        The heat content flux is derived from the fwf flux assuming a temperature set to the freezing point in the top boundary layer (\np{rn_htbl}{rn\_htbl})
+        \item[\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = 'oasis'}]:
+        The \forcode{'oasis'} is a prototype of what could be a method to spread precipitation on Antarctic ice sheet as ice shelf melt inside the cavity when a coupled model Atmosphere/Ocean is used.
+        It has not been tested and therefore the model will stop if you try to use it.
+        Actions will be undertake in 2020 to build a comprehensive interface to do so for Greenland, Antarctic and ice shelf (cav), ice shelf (par), icebergs, subglacial runoff and runoff.
+        \item[\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '2eq'}]:
+        The heat flux and the fresh water flux (negative for melting) resulting from ice shelf melting/freezing are parameterized following \citet{Grosfeld1997}.
+        This formulation is based on a balance between the vertical diffusive heat flux across the ocean top boundary layer (\autoref{eq:ISOMIP1})
+        and the latent heat due to melting/freezing (\autoref{eq:ISOMIP2}):
+        \begin{equation}
+        \label{eq:ISOMIP1}
+        \mathcal{Q}_h = \rho c_p \gamma (T_w - T_f)
+        \end{equation}
+        \begin{equation}
+        \label{eq:ISOMIP2}
+        q = \frac{-\mathcal{Q}_h}{L_f}
+        \end{equation}
+        where $\mathcal{Q}_h$($W.m^{-2}$) is the heat flux,q($kg.s^{-1}m^{-2}$) the fresh-water flux,
+        $L_f$ the specific latent heat, $T_w$ the temperature averaged over a boundary layer below the ice shelf (explained below),
+        $T_f$ the freezing point using  the  pressure  at  the  ice  shelf  base  and  the  salinity  of the water in the boundary layer,
+        and $\gamma$ the thermal exchange coefficient.
+        \item[\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '3eq'}]:
+        For realistic studies, the heat and freshwater fluxes are parameterized following \citep{Jenkins2001}. This formulation is based on three equations:
+        a balance between the vertical diffusive heat flux across the boundary layer
+        , the latent heat due to melting/freezing of ice and the vertical diffusive heat flux into the ice shelf (\autoref{eq:3eq1});
+        a balance between the vertical diffusive salt flux across the boundary layer and the salt source or sink represented by the melting/freezing (\autoref{eq:3eq2});
+        and a linear equation for the freezing temperature of sea water (\autoref{eq:3eq3}, detailed of the linearisation coefficient in \citet{AsayDavis2016}):
+        \begin{equation}
+        \label{eq:3eq1}
+        c_p \rho \gamma_T (T_w-T_b) = -L_f q - \rho_i c_{p,i} \kappa \frac{T_s - T_b}{h_{isf}}
+        \end{equation}
+        \begin{equation}
+        \label{eq:3eq2}
+        \rho \gamma_S (S_w - S_b) = (S_i - S_b)q
+        \end{equation}
+        \begin{equation}
+        \label{eq:3eq3}
+        T_b = \lambda_1 S_b + \lambda_2 +\lambda_3 z_{isf}
+        \end{equation}
+        where $T_b$ is the temperature at the interface, $S_b$ the salinity at the interface, $\gamma_T$ and $\gamma_S$ the exchange coefficients for temperature and salt, respectively,
+        $S_i$ the salinity of the ice (assumed to be 0), $h_{isf}$ the ice shelf thickness, $z_{isf}$ the ice shelf draft, $\rho_i$ the density of the iceshelf,
+        $c_{p,i}$ the specific heat capacity of the ice, $\kappa$ the thermal diffusivity of the ice
+        and $T_s$ the atmospheric surface temperature (at the ice/air interface, assumed to be -20C).
+        The Liquidus slope ($\lambda_1$), the liquidus intercept ($\lambda_2$) and the Liquidus pressure coefficient ($\lambda_3$)
+        for TEOS80 and TEOS10 are described in \citep{AsayDavis2016} and in \citep{Jourdain2017}.
+        The linear system formed by \autoref{eq:3eq1}, \autoref{eq:3eq2} and the linearised equation for the freezing temperature of sea water (\autoref{eq:3eq3}) can be solved for $S_b$ or $T_b$.
+        Afterward, the freshwater flux ($q$) and the heat flux ($\mathcal{Q}_h$) can be computed.
+     \end{description}
+     \begin{table}[h]
+        \centering
+        \caption{Description of the parameters hard coded into the ISF module}
+        \label{tab:isf}
+        \begin{tabular}{|l|l|l|l|}
+        \hline
+        Symbol    & Description               & Value              & Unit               \\
+        \hline
+        $C_p$     & Ocean specific heat       & 3992               & $J.kg^{-1}.K^{-1}$ \\
+        $L_f$     & Ice latent heat of fusion & $3.34 \times 10^5$ & $J.kg^{-1}$        \\
+        $C_{p,i}$ & Ice specific heat         & 2000               & $J.kg^{-1}.K^{-1}$ \\
+        $\kappa$  & Heat diffusivity          & $1.54 \times 10^{-6}$& $m^2.s^{-1}$     \\
+        $\rho_i$  & Ice density               & 920                & $kg.m^3$           \\
+        \hline
+        \end{tabular}
+     \end{table}
+     Temperature and salinity used to compute the fluxes in \autoref{eq:ISOMIP1}, \autoref{eq:3eq1} and \autoref{eq:3eq2} are the average temperature in the top boundary layer \citep{losch_JGR08}.
+     Its thickness is defined by \np{rn_htbl}{rn\_htbl}.
+     The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the first \np{rn_htbl}{rn\_htbl} m.
+     Then, the fluxes are spread over the same thickness (ie over one or several cells).
+     If \np{rn_htbl}{rn\_htbl} is larger than top $e_{3}t$, there is no more direct feedback between the freezing point at the interface and the top cell temperature.
+     This can lead to super-cool temperature in the top cell under melting condition.
+     If \np{rn_htbl}{rn\_htbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\
+     Each melt formula (\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '3eq'} or \np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '2eq'}) depends on an exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice.
+     Below, the exchange coeficient $\Gamma^{T}$ and $\Gamma^{S}$ are respectively defined by \np{rn_gammat0}{rn\_gammat0} and \np{rn_gammas0}{rn\_gammas0}.
+     There are 3 different ways to compute the exchange velocity:
+     \begin{description}
+        \item[\np{cn_gammablk}{cn\_gammablk}\forcode{='spe'}]:
+        The salt and heat exchange coefficients are constant and defined by:
+\[
+\gamma^{T} = \Gamma^{T}
+\]
+\[
+\gamma^{S} = \Gamma^{S}
+\]
+        This is the recommended formulation for ISOMIP.
+   \item[\np{cn_gammablk}{cn\_gammablk}\forcode{='vel'}]:
+        The salt and heat exchange coefficients are velocity dependent and defined as
+\[
+\gamma^{T} = \Gamma^{T} \times u_{*}
+\]
+\[
+\gamma^{S} = \Gamma^{S} \times u_{*}
+\]
+        where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_htbl}{rn\_htbl} meters).
+        See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application and ISOMIP+/MISOMIP configuration.
+   \item[\np{cn_gammablk}{cn\_gammablk}\forcode{'vel\_stab'}]:
+        The salt and heat exchange coefficients are velocity and stability dependent and defined as:
+\[
+\gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}}
+\]
+        where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_tbl}{rn\_htbl} meters),
+        $\Gamma_{Turb}$ the contribution of the ocean stability and
+        $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion.
+        See \citet{holland.jenkins_JPO99} for all the details on this formulation.
+        This formulation has not been extensively tested in NEMO (not recommended).
+     \end{description}
+\subsection{Ocean/Ice shelf fluxes in parametrised cavities}
   \begin{description}
+  \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: The melt rate is based on a balance between the upward ocean heat flux and
+    the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}.
+  \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: The melt rate and the heat flux are based on a 3 equations formulation
+    (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation).
+    A complete description is available in \citet{jenkins_JGR91}.
+     \item[\np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'bg03'}]:
+     The ice shelf cavities are not represented.
+     The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting.
+     The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL)
+     (\np{sn_isfpar_zmax}{sn\_isfpar\_zmax}) and the base of the ice shelf along the calving front
+     (\np{sn_isfpar_zmin}{sn\_isfpar\_zmin}) as in (\np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'spe'}).
+     The effective melting length (\np{sn_isfpar_Leff}{sn\_isfpar\_Leff}) is read from a file.
+     This parametrisation has not been tested since a while and based on \citet{Favier2019},
+     this parametrisation should probably not be used.
+     \item[\np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'spe'}]:
+     The ice shelf cavity is not represented.
+     The fwf (\np{sn_isfpar_fwf}{sn\_isfpar\_fwf}) is prescribed and distributed along the ice shelf edge between
+     the depth of the average grounding line (GL) (\np{sn_isfpar_zmax}{sn\_isfpar\_zmax}) and
+     the base of the ice shelf along the calving front (\np{sn_isfpar_zmin}{sn\_isfpar\_min}). Convention of the input file is positive toward the ocean (i.e. positive for melting and negative for freezing).
+     The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.
+     \item[\np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'oasis'}]:
+     The \forcode{'oasis'} is a prototype of what could be a method to spread precipitation on Antarctic ice sheet as ice shelf melt inside the cavity when a coupled model Atmosphere/Ocean is used.
+     It has not been tested and therefore the model will stop if you try to use it.
+     Action will be undertake in 2020 to build a comprehensive interface to do so for Greenland, Antarctic and ice shelf (cav), ice shelf (par), icebergs, subglacial runoff and runoff.
   \end{description}
+  Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{losch_JGR08}.
+  Its thickness is defined by \np{rn_hisf_tbl}{rn\_hisf\_tbl}.
+  The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the the first \np{rn_hisf_tbl}{rn\_hisf\_tbl} m.
+  Then, the fluxes are spread over the same thickness (ie over one or several cells).
+  If \np{rn_hisf_tbl}{rn\_hisf\_tbl} larger than top $e_{3}t$, there is no more feedback between the freezing point at the interface and the the top cell temperature.
+  This can lead to super-cool temperature in the top cell under melting condition.
+  If \np{rn_hisf_tbl}{rn\_hisf\_tbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\
+  Each melt bulk formula depends on a exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice.
+  There are 3 different ways to compute the exchange coeficient:
+  \begin{description}
+  \item [{\np[=0]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are constant and defined by \np{rn_gammas0}{rn\_gammas0} and \np{rn_gammat0}{rn\_gammat0}.
+    \begin{gather*}
+       % \label{eq:SBC_isf_gamma_iso}
+      \gamma^{T} = rn\_gammat0 \\
+      \gamma^{S} = rn\_gammas0
+    \end{gather*}
+    This is the recommended formulation for ISOMIP.
+  \item [{\np[=1]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity dependent and defined as
+    \begin{gather*}
+      \gamma^{T} = rn\_gammat0 \times u_{*} \\
+      \gamma^{S} = rn\_gammas0 \times u_{*}
+    \end{gather*}
+    where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters).
+    See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application.
+  \item [{\np[=2]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity and stability dependent and defined as:
+    \[
+      \gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}}
+    \]
+    where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters),
+    $\Gamma_{Turb}$ the contribution of the ocean stability and
+    $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion.
+    See \citet{holland.jenkins_JPO99} for all the details on this formulation.
+    This formulation has not been extensively tested in \NEMO\ (not recommended).
+  \end{description}
+\item [{\np[=2]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented.
+  The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting.
+  The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL)
+  (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front
+  (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np[=3]{nn_isf}{nn\_isf}).
+  The effective melting length (\np{sn_Leff_isf}{sn\_Leff\_isf}) is read from a file.
+\item [{\np[=3]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented.
+  The fwf (\np{sn_rnfisf}{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between
+  the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and
+  the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}).
+  The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.
+\item [{\np[=4]{nn_isf}{nn\_isf}}]: The ice shelf cavity is opened (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed).
+  However, the fwf is not computed but specified from file \np{sn_fwfisf}{sn\_fwfisf}).
+  The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.
+  As in \np[=1]{nn_isf}{nn\_isf}, the fluxes are spread over the top boundary layer thickness (\np{rn_hisf_tbl}{rn\_hisf\_tbl})
+\end{description}
+$\bullet$ \np[=1]{nn_isf}{nn\_isf} and \np[=2]{nn_isf}{nn\_isf} compute a melt rate based on
+\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '2eq'}, \np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '3eq'} and \np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'bg03'} compute a melt rate based on
 the water mass properties, ocean velocities and depth.
 This flux is thus highly dependent of the model resolution (horizontal and vertical),
 realism of the water masses onto the shelf ...\\
 $\bullet$ \np[=3]{nn_isf}{nn\_isf} and \np[=4]{nn_isf}{nn\_isf} read the melt rate from a file.
+The resulting fluxes are thus highly dependent of the model resolution (horizontal and vertical) and
+realism of the water masses onto the shelf.\\
+\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = 'spe'} and \np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'spe'} read the melt rate from a file.
 You have total control of the fwf forcing.
 This can be useful if the water masses on the shelf are not realistic or
 the resolution (horizontal/vertical) are too coarse to have realistic melting or
+for studies where you need to control your heat and fw input.\\
+The ice shelf melt is implemented as a volume flux as for the runoff.
+The fw addition due to the ice shelf melting is, at each relevant depth level, added to
+the horizontal divergence (\textit{hdivn}) in the subroutine \rou{sbc\_isf\_div}, called from \mdl{divhor}.
+for studies where you need to control your heat and fw input.
+However, if your forcing is not consistent with the dynamics below you can reach unrealistic low water temperature.\\
+The ice shelf fwf is implemented as a volume flux as for the runoff.
+The fwf addition due to the ice shelf melting is, at each relevant depth level, added to
+the horizontal divergence (\textit{hdivn}) in the subroutine \rou{isf\_hdiv}, called from \mdl{divhor}.
 See the runoff section \autoref{sec:SBC_rnf} for all the details about the divergence correction.\\
+Description and result of sensitivity tests to \np{ln_isfcav_mlt}{ln\_isfcav\_mlt} and \np{ln_isfpar_mlt}{ln\_isfpar\_mlt} are presented in \citet{mathiot.jenkins.ea_GMD17}.
+The different options are illustrated in \autoref{fig:ISF}.
 \begin{figure}[!t]
   \centering
   \includegraphics[width=0.66\textwidth]{SBC_isf}
+  \includegraphics[width=0.66\textwidth]{SBC_isf_v4.2}
   \caption[Ice shelf location and fresh water flux definition]{
     Illustration of the location where the fwf is injected and
     whether or not the fwf is interactif or not depending of \protect\np{nn_isf}{nn\_isf}.}
   \label{fig:SBC_isf}
+    whether or not the fwf is interactive or not.}
+  \label{fig:ISF}
 \end{figure}
+%% =================================================================================================
+\section{Ice sheet coupling}
+\label{sec:SBC_iscpl}
+\begin{listing}
+  \nlst{namsbc_iscpl}
+  \caption{\forcode{&namsbc_iscpl}}
+  \label{lst:namsbc_iscpl}
+\end{listing}
+\subsection{Available outputs}
+The following outputs are availables via XIOS:
+\begin{description}
+   \item[for parametrised cavities]:
+      \begin{xmllines}
+ <field id="isftfrz_par"     long_name="freezing point temperature in the parametrization boundary layer" unit="degC"     />
+ <field id="fwfisf_par"      long_name="Ice shelf melt rate"                           unit="kg/m2/s"  />
+ <field id="qoceisf_par"     long_name="Ice shelf ocean  heat flux"                    unit="W/m2"     />
+ <field id="qlatisf_par"     long_name="Ice shelf latent heat flux"                    unit="W/m2"     />
+ <field id="qhcisf_par"      long_name="Ice shelf heat content flux of injected water" unit="W/m2"     />
+ <field id="fwfisf3d_par"    long_name="Ice shelf melt rate"                           unit="kg/m2/s"  grid_ref="grid_T_3D" />
+ <field id="qoceisf3d_par"   long_name="Ice shelf ocean  heat flux"                    unit="W/m2"     grid_ref="grid_T_3D" />
+ <field id="qlatisf3d_par"   long_name="Ice shelf latent heat flux"                    unit="W/m2"     grid_ref="grid_T_3D" />
+ <field id="qhcisf3d_par"    long_name="Ice shelf heat content flux of injected water" unit="W/m2"     grid_ref="grid_T_3D" />
+ <field id="ttbl_par"        long_name="temperature in the parametrisation boundary layer" unit="degC" />
+ <field id="isfthermald_par" long_name="thermal driving of ice shelf melting"          unit="degC"     />
+      \end{xmllines}
+   \item[for open cavities]:
+      \begin{xmllines}
+ <field id="isftfrz_cav"     long_name="freezing point temperature at ocean/isf interface"                unit="degC"     />
+ <field id="fwfisf_cav"      long_name="Ice shelf melt rate"                           unit="kg/m2/s"  />
+ <field id="qoceisf_cav"     long_name="Ice shelf ocean  heat flux"                    unit="W/m2"     />
+ <field id="qlatisf_cav"     long_name="Ice shelf latent heat flux"                    unit="W/m2"     />
+ <field id="qhcisf_cav"      long_name="Ice shelf heat content flux of injected water" unit="W/m2"     />
+ <field id="fwfisf3d_cav"    long_name="Ice shelf melt rate"                           unit="kg/m2/s"  grid_ref="grid_T_3D" />
+ <field id="qoceisf3d_cav"   long_name="Ice shelf ocean  heat flux"                    unit="W/m2"     grid_ref="grid_T_3D" />
+ <field id="qlatisf3d_cav"   long_name="Ice shelf latent heat flux"                    unit="W/m2"     grid_ref="grid_T_3D" />
+ <field id="qhcisf3d_cav"    long_name="Ice shelf heat content flux of injected water" unit="W/m2"     grid_ref="grid_T_3D" />
+ <field id="ttbl_cav"        long_name="temperature in Losch tbl"                      unit="degC"     />
+ <field id="isfthermald_cav" long_name="thermal driving of ice shelf melting"          unit="degC"     />
+ <field id="isfgammat"       long_name="Ice shelf heat-transfert velocity"             unit="m/s"      />
+ <field id="isfgammas"       long_name="Ice shelf salt-transfert velocity"             unit="m/s"      />
+ <field id="stbl"            long_name="salinity in the Losh tbl"                      unit="1e-3"     />
+ <field id="utbl"            long_name="zonal current in the Losh tbl at T point"      unit="m/s"      />
+ <field id="vtbl"            long_name="merid current in the Losh tbl at T point"      unit="m/s"      />
+ <field id="isfustar"        long_name="ustar at T point used in ice shelf melting"    unit="m/s"      />
+ <field id="qconisf"         long_name="Conductive heat flux through the ice shelf"    unit="W/m2"     />
+      \end{xmllines}
+\end{description}
+%% =================================================================================================
+\subsection{Ice sheet coupling}
+\label{subsec:ISF_iscpl}
 Ice sheet/ocean coupling is done through file exchange at the restart step.
 At each restart step:
 \begin{enumerate}
 \item the ice sheet model send a new bathymetry and ice shelf draft netcdf file.
 \item a new domcfg.nc file is built using the DOMAINcfg tools.
 \item \NEMO\ run for a specific period and output the average melt rate over the period.
 \item the ice sheet model run using the melt rate outputed in step 4.
 \item go back to 1.
 \end{enumerate}
 If \np[=.true.]{ln_iscpl}{ln\_iscpl}, the isf draft is assume to be different at each restart step with
+At each restart step, the procedure is this one:
+\begin{description}
+\item[Step 1]: the ice sheet model send a new bathymetry and ice shelf draft netcdf file.
+\item[Step 2]: a new domcfg.nc file is built using the DOMAINcfg tools.
+\item[Step 3]: NEMO run for a specific period and output the average melt rate over the period.
+\item[Step 4]: the ice sheet model run using the melt rate outputed in step 3.
+\item[Step 5]: go back to 1.
+\end{description}
+If \np{ln_iscpl}{ln\_iscpl}\forcode{ = .true.}, the isf draft is assume to be different at each restart step with
 potentially some new wet/dry cells due to the ice sheet dynamics/thermodynamics.
 The wetting and drying scheme applied on the restart is very simple and described below for the 6 different possible cases:
+The wetting and drying scheme, applied on the restart, is very simple. The 6 different possible cases for the tracer and ssh are:
 \begin{description}
+\item [Thin a cell down]: T/S/ssh are unchanged and U/V in the top cell are corrected to keep the barotropic transport (bt) constant
+  ($bt_b=bt_n$).
+\item [Enlarge  a cell]: See case "Thin a cell down"
+\item [Dry a cell]: mask, T/S, U/V and ssh are set to 0.
+  Furthermore, U/V into the water column are modified to satisfy ($bt_b=bt_n$).
+\item [Wet a cell]: mask is set to 1, T/S is extrapolated from neighbours, $ssh_n = ssh_b$ and U/V set to 0.
+  If no neighbours, T/S is extrapolated from old top cell value.
+  If no neighbours along i,j and k (both previous test failed), T/S/U/V/ssh and mask are set to 0.
+\item [Dry a column]: mask, T/S, U/V are set to 0 everywhere in the column and ssh set to 0.
+\item [Wet a column]: set mask to 1, T/S is extrapolated from neighbours, ssh is extrapolated from neighbours and U/V set to 0.
+  If no neighbour, T/S/U/V and mask set to 0.
+   \item[Thin a cell]:
+   T/S/ssh are unchanged.
+   \item[Enlarge  a cell]:
+   See case "Thin a cell down"
+   \item[Dry a cell]:
+   Mask, T/S, U/V and ssh are set to 0.
+   \item[Wet a cell]:
+   Mask is set to 1, T/S is extrapolated from neighbours, $ssh_n = ssh_b$.
+   If no neighbours, T/S is extrapolated from old top cell value.
+   If no neighbours along i,j and k (both previous tests failed), T/S/ssh and mask are set to 0.
+   \item[Dry a column]:
+   mask, T/S and ssh are set to 0.
+   \item[Wet a column]:
+   set mask to 1, T/S/ssh are extrapolated from neighbours.
+   If no neighbour, T/S/ssh and mask set to 0.
 \end{description}
+The method described above will strongly affect the barotropic transport under an ice shelf when the geometry change.
+In order to keep the model stable, an adjustment of the dynamics at the initialisation after the coupling step is needed.
+The idea behind this is to keep $\pd[\eta]{t}$ as it should be without change in geometry at the initialisation.
+This will prevent any strong velocity due to large pressure gradient.
+To do so, we correct the horizontal divergence before $\pd[\eta]{t}$ is computed in the first time step.\\
 Furthermore, as the before and now fields are not compatible (modification of the geometry),
 …
 The horizontal extrapolation to fill new cell with realistic value is called \np{nn_drown}{nn\_drown} times.
 It means that if the grounding line retreat by more than \np{nn_drown}{nn\_drown} cells between 2 coupling steps,
 the code will be unable to fill all the new wet cells properly.
+the code will be unable to fill all the new wet cells properly and the model is likely to blow up at the initialisation.
 The default number is set up for the MISOMIP idealised experiments.
 This coupling procedure is able to take into account grounding line and calving front migration.
 However, it is a non-conservative processe.
+However, it is a non-conservative proccess.
 This could lead to a trend in heat/salt content and volume.\\
 In order to remove the trend and keep the conservation level as close to 0 as possible,
+a simple conservation scheme is available with \np[=.true.]{ln_hsb}{ln\_hsb}.
+The heat/salt/vol. gain/loss is diagnosed, as well as the location.
+A correction increment is computed and apply each time step during the next \np{rn_fiscpl}{rn\_fiscpl} time steps.
+For safety, it is advised to set \np{rn_fiscpl}{rn\_fiscpl} equal to the coupling period (smallest increment possible).
+The corrective increment is apply into the cell itself (if it is a wet cell), the neigbouring cells or the closest wet cell (if the cell is now dry).
+a simple conservation scheme is available with \np{ln_isfcpl_cons}{ln\_isfcpl\_cons}\forcode{ = .true.}.
+The heat/salt/vol. gain/loss are diagnosed, as well as the location.
+A correction increment is computed and applied each time step during the model run.
+The corrective increment are applied into the cells itself (if it is a wet cell), the neigbouring cells or the closest wet cell (if the cell is now dry).
 %% =================================================================================================
 …
 Melt water (and other variables on the configuration grid) are written into the main \NEMO\ model output files.
+By default, iceberg thermodynamic and dynamic are computed using ocean surface variable (sst, ssu, ssv) and the icebergs are not sensible to the bathymetry (only to land) whatever the iceberg draft.
+\citet{Merino_OM2016} developed an option to use vertical profiles of ocean currents and temperature instead (\np{ln_M2016}{ln\_M2016}).
+Full details on the sensitivity to this parameter in done in \citet{Merino_OM2016}.
+If \np{ln_M2016}{ln\_M2016} activated, \np{ln_icb_grd}{ln\_icb\_grd} activate (or not) an option to prevent thick icebergs to move across shallow bank (ie shallower than the iceberg draft).
+This option need to be used with care as it could required to either change the distribution to prevent generation of icebergs with draft larger than the bathymetry
+or to build a variable \forcode{maxclass} to prevent NEMO filling the icebergs classes too thick for the local bathymetry.
 Extensive diagnostics can be produced.
 Separate output files are maintained for human-readable iceberg information.
 …
 Then using the routine \rou{sbcblk\_algo\_ncar} and starting from the neutral drag coefficent provided,
 the drag coefficient is computed according to the stable/unstable conditions of the
 air-sea interface following \citet{large.yeager_rpt04}.
+air-sea interface following \citet{large.yeager_trpt04}.
 %% =================================================================================================
 …
 The surface stress felt by the ocean is the atmospheric stress minus the net stress going
 into the waves \citep{janssen.breivik.ea_rpt13}. Therefore, when waves are growing, momentum and energy is spent and is not
+into the waves \citep{janssen.breivik.ea_trpt13}. Therefore, when waves are growing, momentum and energy is spent and is not
 available for forcing the mean circulation, while in the opposite case of a decaying sea
 state, more momentum is available for forcing the ocean.
 …
 \label{subsec:SBC_fwb}
+For global ocean simulation, it can be useful to introduce a control of the mean sea level in order to
+prevent unrealistic drift of the sea surface height due to inaccuracy in the freshwater fluxes.
+In \NEMO, two way of controlling the freshwater budget are proposed:
+\begin{listing}
+  \nlst{namsbc_fwb}
+  \caption{\forcode{&namsbc_fwb}}
+  \label{lst:namsbc_fwb}
+\end{listing}
+For global ocean simulations, it can be useful to introduce a control of the
+mean sea level in order to prevent unrealistic drifting of the sea surface
+height due to unbalanced freshwater fluxes. In \NEMO, two options for
+controlling the freshwater budget are proposed.
 \begin{description}
 \item [{\np[=0]{nn_fwb}{nn\_fwb}}] no control at all.
   The mean sea level is free to drift, and will certainly do so.
 \item [{\np[=1]{nn_fwb}{nn\_fwb}}] global mean \textit{emp} set to zero at each model time step.
+\item [{\np[=0]{nn_fwb}{nn\_fwb}}:] No control at all; the mean sea level is
+  free to drift, and will certainly do so.
+\item [{\np[=1]{nn_fwb}{nn\_fwb}}:] The global mean \textit{emp} is set to zero at each model time step.
   %GS: comment below still relevant ?
   %Note that with a sea-ice model, this technique only controls the mean sea level with linear free surface and no mass flux between ocean and ice (as it is implemented in the current ice-ocean coupling).
+\item [{\np[=2]{nn_fwb}{nn\_fwb}}] freshwater budget is adjusted from the previous year annual mean budget which
+  is read in the \textit{EMPave\_old.dat} file.
+  As the model uses the Boussinesq approximation, the annual mean fresh water budget is simply evaluated from
+  the change in the mean sea level at January the first and saved in the \textit{EMPav.dat} file.
+\item [{\np[=2]{nn_fwb}{nn\_fwb}}:] \textit{emp} is adjusted by adding a
+  spatially uniform, annual-mean freshwater flux that balances the freshwater
+  budget at the end of the previous year; as the model uses the Boussinesq
+  approximation, the freshwater budget can be evaluated from the change in the
+  mean sea level and in the ice and snow mass after the end of each simulation
+  year; at the start of the model run, an initial adjustment flux can be set
+  using parameter \np{rn_rwb0}{rn\_fwb0} in namelist \nam{sbc_fwb}{sbc\_fwb}.
 \end{description}

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_STO.tex

r11693	r14789
5	5	\chapter{Stochastic Parametrization of EOS (STO)}
6	6	\label{chap:STO}
7
8		~~\thispagestyle{plain}~~
9	7
10	8	\chaptertoc

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_TRA.tex

-                      r13476
+                      r14789
 \chapter{Ocean Tracers (TRA)}
 \label{chap:TRA}
-\thispagestyle{plain}
 \chaptertoc
 …
 When \np{nn_geoflx}{nn\_geoflx} is set to 2,
 a spatially varying geothermal heat flux is introduced which is provided in
 the \ifile{geothermal\_heating} NetCDF file
+the \textit{geothermal\_heating.nc} NetCDF file
 (\autoref{fig:TRA_geothermal}) \citep{emile-geay.madec_OS09}.
 …
 \citep{madec.delecluse.ea_JPO96}.
 For generating \ifile{resto},
+For generating \textit{resto.nc},
 see the documentation for the DMP tools provided with the source code under \path{./tools/DMP_TOOLS}.
 …
 $\gamma$ is initialized as \np{rn_atfp}{rn\_atfp}, its default value is \forcode{10.e-3}.
 Note that the forcing correction term in the filter is not applied in linear free surface
 (\jp{ln\_linssh}\forcode{=.true.}) (see \autoref{subsec:TRA_sbc}).
+(\np[=.true.]{ln_linssh}{ln\_linssh}) (see \autoref{subsec:TRA_sbc}).
 Not also that in constant volume case, the time stepping is performed on $T$,
 not on its content, $e_{3t}T$.

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_ZDF.tex

-                      r13461
+                      r14789
 \documentclass[../main/NEMO_manual]{subfiles}
-%% Custom aliases
-\newcommand{\cf}{\ensuremath{C\kern-0.14em f}}
 \begin{document}
 …
 \chapter{Vertical Ocean Physics (ZDF)}
 \label{chap:ZDF}
-\thispagestyle{plain}
 \chaptertoc
 …
 $\bar{e}_o = e_{bb} |\tau| / \rho_o$, with $e_{bb}$ the \np{rn_ebb}{rn\_ebb} namelist parameter.
 The default value of $e_{bb}$ is 3.75. \citep{gaspar.gregoris.ea_JGR90}), however a much larger value can be used when
 taking into account the surface wave breaking (see below Eq. \autoref{eq:ZDF_Esbc}).
+taking into account the surface wave breaking (see below \autoref{eq:ZDF_Esbc}).
 The bottom value of TKE is assumed to be equal to the value of the level just above.
 The time integration of the $\bar{e}$ equation may formally lead to negative values because
 …
 the TKE case described in \autoref{subsec:ZDF_tke_ene} \citep{burchard_OM02}.
 Evaluation of the 4 GLS turbulent closure schemes can be found in \citet{warner.sherwood.ea_OM05} in ROMS model and
  in \citet{reffray.guillaume.ea_GMD15} for the \NEMO\ model.
+ in \citet{reffray.bourdalle-badie.ea_GMD15} for the \NEMO\ model.
 % -------------------------------------------------------------------------------------------------------------
 …
 Obsolete namelist parameters include:
 \begin{description}
    \item \protect\np{ln_use_osm_la}\np{ln\_use\_osm\_la} With \protect\np[=0]{nn_osm_wave}{nn\_osm\_wave},
       \protect\np{rn_osm_dstokes} {rn\_osm\_dstokes} is always used to specify the Stokes
       penetration depth.
    \item \protect\np{nn_ave} {nn\_ave} Choice of averaging method for KPP-style Ri \#
       mixing. Not taken account of.
    \item \protect\np{rn_osm_hbl0} {rn\_osm\_hbl0} Depth of initial boundary layer is now set
      by a density criterion similar to that used in calculating \emph{hmlp} (output as \texttt{mldr10\_1}) in \mdl{zdfmxl}.
+\item \protect\np{ln_use_osm_la}\np{ln\_use\_osm\_la} With \protect\np[=0]{nn_osm_wave}{nn\_osm\_wave},
+  \protect\np{rn_osm_dstokes} {rn\_osm\_dstokes} is always used to specify the Stokes
+  penetration depth.
+\item \protect\np{nn_ave} {nn\_ave} Choice of averaging method for KPP-style Ri \#
+  mixing. Not taken account of.
+\item \protect\np{rn_osm_hbl0} {rn\_osm\_hbl0} Depth of initial boundary layer is now set
+  by a density criterion similar to that used in calculating \emph{hmlp} (output as \texttt{mldr10\_1}) in \mdl{zdfmxl}.
 \end{description}
 …
 classical shear turbulence. Instead they are in a regime known as
 `Langmuir turbulence',  dominated by an
 interaction between the currents and the Stokes drift of the surface waves \citep[e.g.][]{mcwilliams.ea_JFM97}.
+interaction between the currents and the Stokes drift of the surface waves \citep[e.g.][]{mcwilliams.sullivan.ea_JFM97}.
 This regime is characterised by strong vertical turbulent motion, and appears when the surface Stokes drift $u_{s0}$ is much greater than the friction velocity $u_{\ast}$. More specifically Langmuir turbulence is thought to be crucial where the turbulent Langmuir number $\mathrm{La}_{t}=(u_{\ast}/u_{s0}) > 0.4$.
 …
 The OSMOSIS turbulent closure scheme is a similarity-scale scheme in
 the same spirit as the K-profile
 parameterization (KPP) scheme of \citet{large.ea_RG97}.
+parameterization (KPP) scheme of \citet{large.mcwilliams.ea_RG94}.
 A specified shape of diffusivity, scaled by the (OSBL) depth
 $h_{\mathrm{BL}}$ and a turbulent velocity scale, is imposed throughout the
 …
 as in KPP, it is set by a prognostic equation that is informed by
 energy budget considerations reminiscent of the classical mixed layer
 models of \citet{kraus.turner_tellus67}.
+models of \citet{kraus.turner_T67}.
 The model also includes an explicit parametrization of the structure
 of the pycnocline (the stratified region at the bottom of the OSBL).
 Presently, mixing below the OSBL is handled by the Richardson
 number-dependent mixing scheme used in \citet{large.ea_RG97}.
 Convective parameterizations such as described in \ref{sec:ZDF_conv}
+number-dependent mixing scheme used in \citet{large.mcwilliams.ea_RG94}.
+Convective parameterizations such as described in \autoref{sec:ZDF_conv}
 below should not be used with the OSMOSIS-OBL model: instabilities
 within the OSBL are part of the model, while instabilities below the
 …
 \subsubsection{Depth and velocity scales}
 The model supposes a boundary layer of thickness $h_{\mathrm{bl}}$ enclosing a well-mixed layer of thickness $h_{\mathrm{ml}}$ and a relatively thin pycnocline at the base of thickness $\Delta h$; Fig.~\ref{fig: OSBL_structure} shows typical (a) buoyancy structure and (b) turbulent buoyancy flux profile for the unstable boundary layer (losing buoyancy at the surface; e.g.\ cooling).
+The model supposes a boundary layer of thickness $h_{\mathrm{bl}}$ enclosing a well-mixed layer of thickness $h_{\mathrm{ml}}$ and a relatively thin pycnocline at the base of thickness $\Delta h$; \autoref{fig:OSBL_structure} shows typical (a) buoyancy structure and (b) turbulent buoyancy flux profile for the unstable boundary layer (losing buoyancy at the surface; e.g.\ cooling).
 \begin{figure}[!t]
   \begin{center}
     %\includegraphics[width=0.7\textwidth]{ZDF_OSM_structure_of_OSBL}
     \caption{
       \protect\label{fig: OSBL_structure}
+      \protect\label{fig:OSBL_structure}
      The structure of the entraining  boundary layer. (a) Mean buoyancy profile. (b) Profile of the buoyancy flux.
+    }
 …
 Consideration of the power input by wind acting on the Stokes drift suggests that the Langmuir turbulence has velocity scale:
+\begin{equation}\label{eq:w_La}
+w_{*L}= \left(u_*^2 u_{s\,0}\right)^{1/3};
+\begin{equation}
+  \label{eq:ZDF_w_La}
+  w_{*L}= \left(u_*^2 u_{s\,0}\right)^{1/3};
 \end{equation}
 but at times the Stokes drift may be weak due to e.g.\ ice cover, short fetch, misalignment with the surface stress, etc.\ so  a composite velocity scale is assumed for the stable (warming) boundary layer:
+\begin{equation}\label{eq:composite-nu}
+\begin{equation}
+  \label{eq:ZDF_composite-nu}
   \nu_{\ast}= \left\{ u_*^3 \left[1-\exp(-.5 \mathrm{La}_t^2)\right]+w_{*L}^3\right\}^{1/3}.
 \end{equation}
 For the unstable boundary layer this is merged with the standard convective velocity scale $w_{*C}=\left(\overline{w^\prime b^\prime}_0 \,h_\mathrm{ml}\right)^{1/3}$, where $\overline{w^\prime b^\prime}_0$ is the upwards surface buoyancy flux, to give:
+\begin{equation}\label{eq:vel-scale-unstable}
+\omega_* = \left(\nu_*^3 + 0.5 w_{*C}^3\right)^{1/3}.
+\begin{equation}
+  \label{eq:ZDF_vel-scale-unstable}
+  \omega_* = \left(\nu_*^3 + 0.5 w_{*C}^3\right)^{1/3}.
 \end{equation}
 \subsubsection{The flux gradient model}
 The flux-gradient relationships used in the OSMOSIS scheme take the form:
+%
+\begin{equation}\label{eq:flux-grad-gen}
+\overline{w^\prime\chi^\prime}=-K\frac{\partial\overline{\chi}}{\partial z} + N_{\chi,s} +N_{\chi,b} +N_{\chi,t},
+\end{equation}
+%
+\begin{equation}
+  \label{eq:ZDF_flux-grad-gen}
+  \overline{w^\prime\chi^\prime}=-K\frac{\partial\overline{\chi}}{\partial z} + N_{\chi,s} +N_{\chi,b} +N_{\chi,t},
+\end{equation}
 where $\chi$ is a general variable and $N_{\chi,s}, N_{\chi,b} \mathrm{and} N_{\chi,t}$  are the non-gradient terms, and represent the effects of the different terms in the turbulent flux-budget on the transport of $\chi$. $N_{\chi,s}$ represents the effects that the Stokes shear has on the transport of $\chi$, $N_{\chi,b}$  the effect of buoyancy, and $N_{\chi,t}$ the effect of the turbulent transport.  The same general form for the flux-gradient relationship is used to parametrize the transports of momentum, heat and salinity.
 In terms of the non-dimensionalized depth variables
+%
+\begin{equation}\label{eq:sigma}
+\sigma_{\mathrm{ml}}= -z/h_{\mathrm{ml}}; \;\sigma_{\mathrm{bl}}= -z/h_{\mathrm{bl}},
+\end{equation}
+%
+\begin{equation}
+  \label{eq:ZDF_sigma}
+  \sigma_{\mathrm{ml}}= -z/h_{\mathrm{ml}}; \;\sigma_{\mathrm{bl}}= -z/h_{\mathrm{bl}},
+\end{equation}
 in unstable conditions the eddy diffusivity ($K_d$) and eddy viscosity ($K_\nu$) profiles are parametrized as:
+%
+\begin{align}\label{eq:diff-unstable}
+K_d=&0.8\, \omega_*\, h_{\mathrm{ml}} \, \sigma_{\mathrm{ml}} \left(1-\beta_d \sigma_{\mathrm{ml}}\right)^{3/2}
+\\\label{eq:visc-unstable}
+K_\nu =& 0.3\, \omega_* \,h_{\mathrm{ml}}\, \sigma_{\mathrm{ml}} \left(1-\beta_\nu \sigma_{\mathrm{ml}}\right)\left(1-\tfrac{1}{2}\sigma_{\mathrm{ml}}^2\right)
+\begin{align}
+  \label{eq:ZDF_diff-unstable}
+  K_d=&0.8\, \omega_*\, h_{\mathrm{ml}} \, \sigma_{\mathrm{ml}} \left(1-\beta_d \sigma_{\mathrm{ml}}\right)^{3/2}
+  \\
+  \label{eq:ZDF_visc-unstable}
+  K_\nu =& 0.3\, \omega_* \,h_{\mathrm{ml}}\, \sigma_{\mathrm{ml}} \left(1-\beta_\nu \sigma_{\mathrm{ml}}\right)\left(1-\tfrac{1}{2}\sigma_{\mathrm{ml}}^2\right)
 \end{align}
+%
+where $\beta_d$ and $\beta_\nu$ are parameters that are determined by matching Eqs \ref{eq:diff-unstable} and \ref{eq:visc-unstable} to the eddy diffusivity and viscosity at the base of the well-mixed layer, given by
+%
+\begin{equation}\label{eq:diff-wml-base}
+K_{d,\mathrm{ml}}=K_{\nu,\mathrm{ml}}=\,0.16\,\omega_* \Delta h.
+\end{equation}
+%
+where $\beta_d$ and $\beta_\nu$ are parameters that are determined by matching \autoref{eq:ZDF_diff-unstable} and \autoref{eq:ZDF_visc-unstable} to the eddy diffusivity and viscosity at the base of the well-mixed layer, given by
+\begin{equation}
+  \label{eq:ZDF_diff-wml-base}
+  K_{d,\mathrm{ml}}=K_{\nu,\mathrm{ml}}=\,0.16\,\omega_* \Delta h.
+\end{equation}
 For stable conditions the eddy diffusivity/viscosity profiles are given by:
+%
+\begin{align}\label{diff-stable}
+K_d= & 0.75\,\, \nu_*\, h_{\mathrm{ml}}\,\,  \exp\left[-2.8 \left(h_{\mathrm{bl}}/L_L\right)^2\right]\sigma_{\mathrm{ml}} \left(1-\sigma_{\mathrm{ml}}\right)^{3/2} \\\label{eq:visc-stable}
+K_\nu = & 0.375\,\,  \nu_*\, h_{\mathrm{ml}} \,\, \exp\left[-2.8 \left(h_{\mathrm{bl}}/L_L\right)^2\right] \sigma_{\mathrm{ml}} \left(1-\sigma_{\mathrm{ml}}\right)\left(1-\tfrac{1}{2}\sigma_{\mathrm{ml}}^2\right).
+\begin{align}
+  \label{eq:ZDF_diff-stable}
+  K_d= & 0.75\,\, \nu_*\, h_{\mathrm{ml}}\,\,  \exp\left[-2.8
+       \left(h_{\mathrm{bl}}/L_L\right)^2\right]\sigma_{\mathrm{ml}}
+       \left(1-\sigma_{\mathrm{ml}}\right)^{3/2} \\
+  \label{eq:ZDF_visc-stable}
+  K_\nu = & 0.375\,\,  \nu_*\, h_{\mathrm{ml}} \,\, \exp\left[-2.8 \left(h_{\mathrm{bl}}/L_L\right)^2\right] \sigma_{\mathrm{ml}} \left(1-\sigma_{\mathrm{ml}}\right)\left(1-\tfrac{1}{2}\sigma_{\mathrm{ml}}^2\right).
 \end{align}
+%
 The shape of the eddy viscosity and diffusivity profiles is the same as the shape in the unstable OSBL. The eddy diffusivity/viscosity depends on the stability parameter $h_{\mathrm{bl}}/{L_L}$ where $ L_L$ is analogous to the Obukhov length, but for Langmuir turbulence:
+\begin{equation}\label{eq:L_L}
+\begin{equation}
+  \label{eq:ZDF_L_L}
   L_L=-w_{*L}^3/\left<\overline{w^\prime b^\prime}\right>_L,
 \end{equation}
 with the mean turbulent buoyancy flux averaged over the boundary layer given in terms of its surface value $\overline{w^\prime b^\prime}_0$ and (downwards) )solar irradiance $I(z)$ by
+\begin{equation} \label{eq:stable-av-buoy-flux}
+\left<\overline{w^\prime b^\prime}\right>_L = \tfrac{1}{2} {\overline{w^\prime b^\prime}}_0-g\alpha_E\left[\tfrac{1}{2}(I(0)+I(-h))-\left<I\right>\right].
+\end{equation}
+%
+\begin{equation}
+  \label{eq:ZDF_stable-av-buoy-flux}
+  \left<\overline{w^\prime b^\prime}\right>_L = \tfrac{1}{2} {\overline{w^\prime b^\prime}}_0-g\alpha_E\left[\tfrac{1}{2}(I(0)+I(-h))-\left<I\right>\right].
+\end{equation}
 In unstable conditions the eddy diffusivity and viscosity depend on stability through the velocity scale $\omega_*$, which depends on the two velocity scales $\nu_*$ and $w_{*C}$.
 Details of the non-gradient terms in \eqref{eq:flux-grad-gen} and of the fluxes within the pycnocline $-h_{\mathrm{bl}}<z<h_{\mathrm{ml}}$ can be found in Grant (2019).
+Details of the non-gradient terms in \autoref{eq:ZDF_flux-grad-gen} and of the fluxes within the pycnocline $-h_{\mathrm{bl}}<z<h_{\mathrm{ml}}$ can be found in Grant (2019).
 \subsubsection{Evolution of the boundary layer depth}
+The prognostic equation for the depth of the neutral/unstable boundary layer is given by \citep{grant+etal18},
+\begin{equation} \label{eq:dhdt-unstable}
+The prognostic equation for the depth of the neutral/unstable boundary layer is given by \iffalse \citep{grant+etal18?}, \fi
+\begin{equation}
+  \label{eq:ZDF_dhdt-unstable}
 %\frac{\partial h_\mathrm{bl}}{\partial t} + \mathbf{U}_b\cdot\nabla h_\mathrm{bl}= W_b - \frac{{\overline{w^\prime b^\prime}}_\mathrm{ent}}{\Delta B_\mathrm{bl}}
 \frac{\partial h_\mathrm{bl}}{\partial t} = W_b - \frac{{\overline{w^\prime b^\prime}}_\mathrm{ent}}{\Delta B_\mathrm{bl}}
+   \frac{\partial h_\mathrm{bl}}{\partial t} = W_b - \frac{{\overline{w^\prime b^\prime}}_\mathrm{ent}}{\Delta B_\mathrm{bl}}
 \end{equation}
 where $h_\mathrm{bl}$ is the horizontally-varying depth of the OSBL,
 …
 equation for the case when the pycnocline has a finite thickness,
 based on the potential energy budget of the OSBL, is the leading term
 \citep{grant+etal18} of a generalization of that used in mixed-layer
 models e.g.\ \citet{kraus.turner_tellus67}, in which the thickness of the pycnocline is taken to be zero.
+\iffalse \citep{grant+etal18?} \fi of a generalization of that used in mixed-layer
+models e.g.\ \citet{kraus.turner_T67}, in which the thickness of the pycnocline is taken to be zero.
 The entrainment flux for the combination of convective and Langmuir turbulence is given by
+\begin{equation} \label{eq:entrain-flux}
+\begin{equation}
+  \label{eq:ZDF_entrain-flux}
   {\overline{w^\prime b^\prime}}_\mathrm{ent} = -\alpha_{\mathrm{B}} {\overline{w^\prime b^\prime}}_0 - \alpha_{\mathrm{S}} \frac{u_*^3}{h_{\mathrm{ml}}}
   + G\left(\delta/h_{\mathrm{ml}} \right)\left[\alpha_{\mathrm{S}}e^{-1.5\, \mathrm{La}_t}-\alpha_{\mathrm{L}} \frac{w_{\mathrm{*L}}^3}{h_{\mathrm{ml}}}\right]
 …
 For the stable boundary layer, the equation for the depth of the OSBL is:
+\begin{equation}\label{eq:dhdt-stable}
+\begin{equation}
+  \label{eq:ZDF_dhdt-stable}
 \max\left(\Delta B_{bl},\frac{w_{*L}^2}{h_\mathrm{bl}}\right)\frac{\partial h_\mathrm{bl}}{\partial t} = \left(0.06 + 0.52\,\frac{ h_\mathrm{bl}}{L_L}\right) \frac{w_{*L}^3}{h_\mathrm{bl}} +\left<\overline{w^\prime b^\prime}\right>_L.
 \end{equation}
 Equation. \ref{eq:dhdt-unstable} always leads to the depth of the entraining OSBL increasing (ignoring the effect of the mean vertical motion), but the change in the thickness of the stable OSBL given by Eq. \ref{eq:dhdt-stable} can be positive or negative, depending on the magnitudes of $\left<\overline{w^\prime b^\prime}\right>_L$ and $h_\mathrm{bl}/L_L$. The rate at which the depth of the OSBL can decrease is limited by choosing an effective buoyancy $w_{*L}^2/h_\mathrm{bl}$, in place of $\Delta B_{bl}$ which will be $\approx 0$ for the collapsing OSBL.
+\autoref{eq:ZDF_dhdt-unstable} always leads to the depth of the entraining OSBL increasing (ignoring the effect of the mean vertical motion), but the change in the thickness of the stable OSBL given by \autoref{eq:ZDF_dhdt-stable} can be positive or negative, depending on the magnitudes of $\left<\overline{w^\prime b^\prime}\right>_L$ and $h_\mathrm{bl}/L_L$. The rate at which the depth of the OSBL can decrease is limited by choosing an effective buoyancy $w_{*L}^2/h_\mathrm{bl}$, in place of $\Delta B_{bl}$ which will be $\approx 0$ for the collapsing OSBL.
 …
   \label{lst:namdrg}
 \end{listing}
 \begin{listing}
   \nlst{namdrg_top}
 …
   \label{lst:namdrg_top}
 \end{listing}
 \begin{listing}
   \nlst{namdrg_bot}
 …
 \]
 When \np[=.true.]{ln_lin}{ln\_lin}, the value of $r$ used is \np{rn_Uc0}{rn\_Uc0}*\np{rn_Cd0}{rn\_Cd0}.
 Setting \np[=.true.]{ln_drg_OFF}{ln\_OFF} (and \forcode{ln_lin=.true.}) is equivalent to setting $r=0$ and leads to a free-slip boundary condition.
+Setting \np[=.true.]{ln_drg_OFF}{ln\_drg\_OFF} (and \forcode{ln_lin=.true.}) is equivalent to setting $r=0$ and leads to a free-slip boundary condition.
 These values are assigned in \mdl{zdfdrg}.
 Note that there is support for local enhancement of these values via an externally defined 2D mask array
 (\np[=.true.]{ln_boost}{ln\_boost}) given in the \ifile{bfr\_coef} input NetCDF file.
+(\np[=.true.]{ln_boost}{ln\_boost}) given in the \textit{bfr\_coef.nc} input NetCDF file.
 The mask values should vary from 0 to 1.
 Locations with a non-zero mask value will have the friction coefficient increased by
 …
 by only a few extra physics choices namely:
 \begin{verbatim}
+\begin{forlines}
      ln_dynldf_OFF = .false.
      ln_dynldf_lap = .true.
 …
         nn_fct_h   =  2
         nn_fct_v   =  2
 \end{verbatim}
+\end{forlines}
 \noindent which were chosen to provide a slightly more stable and less noisy solution. The

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_cfgs.tex

-                      r11693
+                      r14789
 \chapter{Configurations}
 \label{chap:CFGS}
-\thispagestyle{plain}
 \chaptertoc
 …
 the SI3 model (ORCA-ICE) and possibly with PISCES biogeochemical model (ORCA-ICE-PISCES).
 An appropriate namelist is available in \path{./cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_cfg} for ORCA2.
 The domain of ORCA2 configuration is defined in \ifile{ORCA\_R2\_zps\_domcfg} file,
+The domain of ORCA2 configuration is defined in \textit{ORCA\_R2\_zps\_domcfg.nc} file,
 this file is available in tar file on the \NEMO\ community zenodo platform: \\
 https://doi.org/10.5281/zenodo.2640723
 …
 Each of configuration is set through the \textit{domain\_cfg} domain configuration file,
 which sets the grid size and configuration name parameters.
 The \NEMO\ System Team provides only ORCA2 domain input file "\ifile{ORCA\_R2\_zps\_domcfg}" file
+The \NEMO\ System Team provides only ORCA2 domain input file "\textit{ORCA\_R2\_zps\_domcfg.nc}" file
 (\autoref{tab:CFGS_ORCA}).
 …
   \centering
   \begin{tabular}{p{4cm} c c c c}
     Horizontal Grid & \jp{ORCA\_index} & \jp{jpiglo} & \jp{jpjglo} \\
+    Horizontal Grid & \texttt{ORCA\_index} & \texttt{jpiglo} & \texttt{jpjglo} \\
     \hline \hline
     % 4   \deg\ &              4   &          92 &          76 \\
 …
 (see \autoref{tab:CFGS_ORCA} and \autoref{fig:DOM_zgr_e3}).
 The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997).
 The default forcing uses the boundary forcing from \citet{large.yeager_rpt04} (see \autoref{subsec:SBC_blk_ocean}),
+The default forcing uses the boundary forcing from \citet{large.yeager_trpt04} (see \autoref{subsec:SBC_blk_ocean}),
 which was developed for the purpose of running global coupled ocean-ice simulations without
 an interactive atmosphere.
 This \citet{large.yeager_rpt04} dataset is available through
+This \citet{large.yeager_trpt04} dataset is available through
 the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
 The "normal year" of \citet{large.yeager_rpt04} has been chosen of the \NEMO\ distribution since release v3.3.
+The "normal year" of \citet{large.yeager_trpt04} has been chosen of the \NEMO\ distribution since release v3.3.
 ORCA\_R2 pre-defined configuration can also be run with multiply online nested zooms (\ie\ with AGRIF, \key{agrif} defined).
 …
 Through \np[=.false.]{ln_read_cfg}{ln\_read\_cfg} in \nam{cfg}{cfg} namelist defined in
 the reference configuration \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}
 analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines.
+analytical definition of grid in GYRE is done in mdl{usrdef\_hrg}, \mdl{usrdef\_zgr} routines.
 Its horizontal resolution (and thus the size of the domain) is determined by
+setting \np{nn_GYRE}{nn\_GYRE} in \nam{usr_def}{usr\_def}: \\
+\jp{jpiglo} $= 30 \times$ \np{nn_GYRE}{nn\_GYRE} + 2   \\
+\jp{jpjglo} $= 20 \times$ \np{nn_GYRE}{nn\_GYRE} + 2   \\
+setting \np{nn_GYRE}{nn\_GYRE} in \nam{usr_def}{usr\_def}:
+\begin{align*}
+   jpiglo = 30 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}} \\
+   jpjglo = 20 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}}
+\end{align*}
 Obviously, the namelist parameters have to be adjusted to the chosen resolution,
 see the Configurations pages on the \NEMO\ web site (\NEMO\ Configurations).
+In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:DOM_zgr_e3}).
+In the vertical, GYRE uses the default 30 ocean levels (\forcode{jpk = 31}, \autoref{fig:DOM_zgr_e3}).
+\begin{listing}
+  \begin{forlines}
+!-----------------------------------------------------------------------
+&namusr_def    !   GYRE user defined namelist
+!-----------------------------------------------------------------------
+   nn_GYRE     =     1     !  GYRE resolution [1/degrees]
+   ln_bench    = .false.   !  ! =T benchmark with gyre: the gridsize is kept constant
+   jpkglo      =    31     !  number of model levels
+/
+  \end{forlines}
+  \caption{\forcode{&namusr_def}}
+  \label{lst:namusr_def}
+\end{listing}
 The GYRE configuration is also used in benchmark test as it is very simple to increase its resolution and

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_conservation.tex

r11693	r14789
5	5	\chapter{Invariants of the Primitive Equations}
6	6	\label{chap:CONS}
7
8		~~\thispagestyle{plain}~~
9	7
10	8	\chaptertoc

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_misc.tex

-                      r12377
+                      r14789
 \label{chap:MISC}
-\thispagestyle{plain}
 \chaptertoc
 …
 {\footnotesize
   \begin{tabularx}{\textwidth}{l||X|X}
     Release & Author(s) & Modifications \\
+    Release     & Author(s)            & Modifications                      \\
     \hline
+    {\em   4.0} & {\em ...} & {\em ...} \\
+    {\em   3.6} & {\em ...} & {\em ...} \\
+    {\em   3.4} & {\em ...} & {\em ...} \\
+    {\em <=3.4} & {\em ...} & {\em ...}
+    {\em   X.X} & {\em Pierre Mathiot} & {Update of the closed sea section} \\
+    {\em   4.0} & {\em ...           } & {\em ...                         } \\
+    {\em   3.6} & {\em ...           } & {\em ...                         } \\
+    {\em   3.4} & {\em ...           } & {\em ...                         } \\
+    {\em <=3.4} & {\em ...           } & {\em ...                         }
   \end{tabularx}
+}
 …
 \end{figure}
-\begin{figure}[!tbp]
-  \centering
-  \includegraphics[width=0.66\textwidth]{MISC_closea_mask_example}
-  \caption[Mask fields for the \protect\mdl{closea} module]{
-    Example of mask fields for the \protect\mdl{closea} module.
-    \textit{Left}: a closea\_mask field;
-    \textit{Right}: a closea\_mask\_rnf field.
-    In this example, if \protect\np{ln_closea}{ln\_closea} is set to \forcode{.true.},
-    the mean freshwater flux over each of the American Great Lakes will be set to zero,
-    and the total residual for all the lakes, if negative, will be put into
-    the St Laurence Seaway in the area shown.}
-  \label{fig:MISC_closea_mask_example}
-\end{figure}
 %% =================================================================================================
 \section[Closed seas (\textit{closea.F90})]{Closed seas (\protect\mdl{closea})}
 \label{sec:MISC_closea}
+\begin{listing}
+  \nlst{namclo}
+  \caption{\forcode{&namclo}}
+  \label{lst:namclo}
+\end{listing}
 Some configurations include inland seas and lakes as ocean
 …
 to zero and put the residual flux into the ocean.
+Prior to \NEMO\ 4 the locations of inland seas and lakes was set via
+hardcoded indices for various ORCA configurations. From \NEMO\ 4 onwards
+the inland seas and lakes are defined using mask fields in the
+domain configuration file. The options are as follows.
+\begin{enumerate}
+\item {{\bfseries No ``closea\_mask'' field is included in domain configuration
+  file.} In this case the closea module does nothing.}
+\item {{\bfseries A field called closea\_mask is included in the domain
+configuration file and ln\_closea=.false. in namelist namcfg.} In this
+case the inland seas defined by the closea\_mask field are filled in
+(turned to land points) at run time. That is every point in
+closea\_mask that is nonzero is set to be a land point.}
+\item {{\bfseries A field called closea\_mask is included in the domain
+configuration file and ln\_closea=.true. in namelist namcfg.} Each
+inland sea or group of inland seas is set to a positive integer value
+in the closea\_mask field (see \autoref{fig:MISC_closea_mask_example}
+for an example). The net surface flux over each inland sea or group of
+The inland seas and lakes are defined using mask fields in the
+domain configuration file. Special treatment of the closed sea (redistribution of net freshwater or mask those), are defined in \autoref{lst:namclo} and
+can be trigger by \np{ln_closea}{ln\_closea}\forcode{=.true.} in namelist namcfg.
+The options available are the following:
+\begin{description}
+\item[\np{ln_maskcs}{ln\_maskcs}\forcode{ = .true.}] All the closed seas are masked using \textit{mask\_opensea} variable.
+\item[\np{ln_maskcs}{ln\_maskcs}\forcode{ = .false.}] The net surface flux over each inland sea or group of
 inland seas is set to zero each timestep and the residual flux is
+distributed over the global ocean (ie. all ocean points where
+closea\_mask is zero).}
+\item {{\bfseries Fields called closea\_mask and closea\_mask\_rnf are
+included in the domain configuration file and ln\_closea=.true. in
+namelist namcfg.} This option works as for option 3, except that if
+the net surface flux over an inland sea is negative (net
+precipitation) it is put into the ocean at specified runoff points. A
+net positive surface flux (net evaporation) is still spread over the
+global ocean. The mapping from inland seas to runoff points is defined
+by the closea\_mask\_rnf field. Each mapping is defined by a positive
+integer value for the inland sea(s) and the corresponding runoff
+points. An example is given in
+\autoref{fig:MISC_closea_mask_example}. If no mapping is provided for a
+particular inland sea then the residual is spread over the global
+ocean.}
+\item {{\bfseries Fields called closea\_mask and closea\_mask\_emp are
+included in the domain configuration file and ln\_closea=.true. in
+namelist namcfg.} This option works the same as option 4 except that
+the nonzero net surface flux is sent to the ocean at the specified
+runoff points regardless of whether it is positive or negative. The
+mapping from inland seas to runoff points in this case is defined by
+the closea\_mask\_emp field.}
+\end{enumerate}
+There is a python routine to create the closea\_mask fields and append
+them to the domain configuration file in the utils/tools/DOMAINcfg directory.
+distributed over a target area.
+\end{description}
+When \np{ln_maskcs}{ln\_maskcs}\forcode{ = .false.},
+options are available for the redistribution (set up of these options is done in the tool DOMAINcfg):
+\begin{description}[font=$\bullet$ ]
+\item[ glo]: The residual flux is redistributed globally.
+\item[ emp]: The residual flux is redistributed as emp in a river outflow.
+\item[ rnf]: The residual flux is redistributed as rnf in a river outflow if negative. If there is a net evaporation, the residual flux is redistributed globally.
+\end{description}
+For each case, 2 masks are needed (\autoref{fig:MISC_closea_mask_example}):
+\begin{description}
+\item $\bullet$ one describing the 'sources' (ie the closed seas concerned by each options) called \textit{mask\_csglo}, \textit{mask\_csrnf}, \textit{mask\_csemp}.
+\item $\bullet$ one describing each group of inland seas (the Great Lakes for example) and the target area (river outflow or world ocean) for each group of inland seas (St Laurence for the Great Lakes for example) called
+\textit{mask\_csgrpglo}, \textit{mask\_csgrprnf}, \textit{mask\_csgrpemp}.
+\end{description}
+\begin{figure}[!tbp]
+  \centering
+  \includegraphics[width=0.66\textwidth]{MISC_closea_mask_example}
+  \caption[Mask fields for the \protect\mdl{closea} module]{
+    Example of mask fields for the \protect\mdl{closea} module.
+    \textit{Left}: a \textit{mask\_csrnf} field;
+    \textit{Right}: a \textit{mask\_csgrprnf} field.
+    In this example, if \protect\np{ln_closea}{ln\_closea} is set to \forcode{.true.},
+    the mean freshwater flux over each of the American Great Lakes will be set to zero,
+    and the total residual for all the lakes, if negative, will be put into
+    the St Laurence Seaway in the area shown.}
+  \label{fig:MISC_closea_mask_example}
+\end{figure}
+Closed sea not defined (because too small, issue in the bathymetry definition ...) are defined in \textit{mask\_csundef}.
+These points can be masked using the namelist option \np{ln_mask_csundef}{ln\_mask\_csundef}\forcode{= .true.} or used to correct the bathymetry input file.\\
+The masks needed for the closed sea can be created using the DOMAINcfg tool in the utils/tools/DOMAINcfg directory.
+See \autoref{sec:clocfg} for details on the usage of definition of the closed sea masks.
 %% =================================================================================================
 …
 \noindent Consider an ORCA1
 configuration using the extended grid domain configuration file: \ifile{eORCA1\_domcfg.nc}
+configuration using the extended grid domain configuration file: \textit{eORCA1\_domcfg.nc}
 This file define a horizontal domain of 362x332.  The first row with
 open ocean wet points in the non-isf bathymetry for this set is row 42 (\fortran\ indexing)
 …
 \noindent Note that with this option, the j-size of the global domain is (extended
 j-size minus \np{open_ocean_jstart}{open\_ocean\_jstart} + 1 ) and this must match the \texttt{jpjglo} value
 for the configuration. This means an alternative version of \ifile{eORCA1\_domcfg.nc} must
+for the configuration. This means an alternative version of \textit{eORCA1\_domcfg.nc} must
 be created for when \np{ln_use_jattr}{ln\_use\_jattr} is active. The \texttt{ncap2} tool provides a
 convenient way of achieving this:
 …
 \end{cmds}
 The domain configuration file is unique in this respect since it also contains the value of \jp{jpjglo}
+The domain configuration file is unique in this respect since it also contains the value of \texttt{jpjglo}
 that is read and used by the model.
 Any other global, 2D and 3D, netcdf, input field can be prepared for use in a reduced domain by adding the
 …
 When more information is required for monitoring or debugging purposes, the various
 forms of output can be selected via the \np{sn\_cfctl} structure. As well as simple
+forms of output can be selected via the \np{sn_cfctl}{sn\_cfctl} structure. As well as simple
 on-off switches this structure also allows selection of a range of processors for
 individual reporting (where appropriate) and a time-increment option to restrict
 …
 with their default settings:
 \begin{verbatim}
+\begin{forlines}
    sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T
      sn_cfctl%l_config = .TRUE.     ! IF .true. then control which reports are written with the following
 \end{verbatim}
+\end{forlines}
 The first switch is a convenience option which can be used to switch on and off all
 sub-options. However, if it is false then switching off all sub-options is only done
 if \texttt{sn_cfctl%l\_config} is also false. Specifically, the logic is:
 \begin{verbatim}
+if \forcode{sn_cfctl%l\_config} is also false. Specifically, the logic is:
+\begin{forlines}
   IF ( sn_cfctl%l_allon ) THEN
     set all suboptions .TRUE.
 …
     set all suboptions .FALSE.
   ENDIF
 \end{verbatim}
+\end{forlines}
 Details of the suboptions follow but first an explanation of the stand-alone option:
 \texttt{sn_cfctl%l_glochk}.  This option modifies the action of the early warning checks
 carried out in \textt{stpctl.F90}. These checks detect probable numerical instabilites
+\forcode{sn_cfctl%l_glochk}.  This option modifies the action of the early warning checks
+carried out in \texttt{stpctl.F90}. These checks detect probable numerical instabilites
 by searching for excessive sea surface heights or velocities and salinity values
 outside a sensible physical range. If breaches are detected then the default behaviour
 is to locate and report the local indices of the grid-point in breach. These indices
 are included in the error message that precedes the model shutdown. When true,
 \texttt{sn_cfctl%l_glochk} modifies this action by performing a global location of
+\forcode{sn_cfctl%l_glochk} modifies this action by performing a global location of
 the various minimum and maximum values and the global indices are reported. This has
 some value in locating the most severe error in cases where the first detected error
 …
 average tracer value for each passive tracer. Collecting these metrics involves
 global communications and will impact on model efficiency so both these options are
 disabled by default by setting the respective options, \texttt{sn\_cfctl%runstat} and
 \texttt{sn\_cfctl%trcstat} to false. A compromise can be made by activating either or
 both of these options and setting the \texttt{sn\_cfctl%timincr} entry to an integer
+disabled by default by setting the respective options, \forcode{sn\_cfctl%runstat} and
+\forcode{sn\_cfctl%trcstat} to false. A compromise can be made by activating either or
+both of these options and setting the \forcode{sn\_cfctl%timincr} entry to an integer
 value greater than one. This increment determines the time-step frequency at which
 the global metrics are collected and reported.  This increment also applies to the
 …
 any warning or error messages generated during execution. A \texttt{layout.dat}
 file is also produced which details the MPI-decomposition used by the model. The
 suboptions: \texttt{sn\_cfctl%oceout} and \texttt{sn\_cfctl%layout} can be used
+suboptions: \forcode{sn\_cfctl%oceout} and \forcode{sn\_cfctl%layout} can be used
 to activate the creation of these files by all ocean processes.  For example,
 when \texttt{sn\_cfctl%oceout} is true all processors produce their own version of
+when \forcode{sn\_cfctl%oceout} is true all processors produce their own version of
 \texttt{ocean.output}.  All files, beyond the the normal reporting processor (narea == 1), are
 named with a \_XXXX extension to their name, where XXXX is a 4-digit area number (with
 …
 systems so bug-hunting efforts using this facility should also utilise the \fortran:
+\begin{verbatim}
+   CALL FLUSH(numout)
+\end{verbatim}
+\forline|CALL FLUSH(numout)|
 statement after any additional write statements to ensure that file contents reflect
 the last model state. Associated with the \texttt{sn\_cfctl%oceout} option is the
 additional \texttt{sn\_cfctl%oasout} suboption. This does not activate its own output
+the last model state. Associated with the \forcode{sn\_cfctl%oceout} option is the
+additional \forcode{sn\_cfctl%oasout} suboption. This does not activate its own output
 file but rather activates the writing of addition information regarding the OASIS
 configuration when coupling via oasis and the sbccpl routine. This information is
 …
 http://forge.ipsl.jussieu.fr/nemo/attachment/wiki/Documentation/prtctl_NEMO_doc_v2.pdf}{The
 control print option in NEMO} The switches to activate production of the control sums
 of trends for either the physics or passive tracers are the \texttt{sn\_cfctl%prtctl}
 and \texttt{sn\_cfctl%prttrc} suboptions, respectively. Although, perhaps, of limited use for its
+of trends for either the physics or passive tracers are the \forcode{sn\_cfctl%prtctl}
+and \forcode{sn\_cfctl%prttrc} suboptions, respectively. Although, perhaps, of limited use for its
 original intention, the ability to produce these control sums of trends in specific
 areas provides another tool for diagnosing model behaviour.  If only the output from a
 select few regions is required then additional options are available to activate options
 for only a simple subset of processing regions. These are: \texttt{sn\_cfctl%procmin},
 \texttt{sn\_cfctl%procmax} and \texttt{sn\_cfctl%procincr} which can be used to specify
+for only a simple subset of processing regions. These are: \forcode{sn\_cfctl%procmin},
+\forcode{sn\_cfctl%procmax} and \forcode{sn\_cfctl%procincr} which can be used to specify
 the minimum and maximum active areas and the increment. The default values are set
 such that all regions will be active. Note this subsetting can also be used to limit
 …
 \end{enumerate}
+   sn_cfctl%l_glochk = .FALSE.    ! Range sanity checks are local (F) or global (T). Set T for debugging only
+   sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T
+     sn_cfctl%l_config = .TRUE.     ! IF .true. then control which reports are written with the following
+       sn_cfctl%l_runstat = .FALSE. ! switches and which areas produce reports with the proc integer settings.
+       sn_cfctl%l_trcstat = .FALSE. ! The default settings for the proc integers should ensure
+       sn_cfctl%l_oceout  = .FALSE. ! that  all areas report.
+       sn_cfctl%l_layout  = .FALSE. !
+       sn_cfctl%l_prtctl  = .FALSE. !
+       sn_cfctl%l_prttrc  = .FALSE. !
+       sn_cfctl%l_oasout  = .FALSE. !
+       sn_cfctl%procmin   = 0       ! Minimum area number for reporting [default:0]
+       sn_cfctl%procmax   = 1000000 ! Maximum area number for reporting [default:1000000]
+       sn_cfctl%procincr  = 1       ! Increment for optional subsetting of areas [default:1]
+       sn_cfctl%ptimincr  = 1       ! Timestep increment for writing time step progress info
+\begin{forlines}
+   sn_cfctl%l_glochk  = .false. ! Range sanity checks are local (F) or global (T). Set T for debugging only
+   sn_cfctl%l_allon   = .false. ! IF T activate all options. If F deactivate all unless l_config is T
+   sn_cfctl%l_config  = .true.  ! IF .true. then control which reports are written with the following
+   sn_cfctl%l_runstat = .false. ! switches and which areas produce reports with the proc integer settings.
+   sn_cfctl%l_trcstat = .false. ! The default settings for the proc integers should ensure
+   sn_cfctl%l_oceout  = .false. ! that  all areas report.
+   sn_cfctl%l_layout  = .false. !
+   sn_cfctl%l_prtctl  = .false. !
+   sn_cfctl%l_prttrc  = .false. !
+   sn_cfctl%l_oasout  = .false. !
+   sn_cfctl%procmin   = 0       ! Minimum area number for reporting [default:0]
+   sn_cfctl%procmax   = 1000000 ! Maximum area number for reporting [default:1000000]
+   sn_cfctl%procincr  = 1       ! Increment for optional subsetting of areas [default:1]
+   sn_cfctl%ptimincr  = 1       ! Timestep increment for writing time step progress info
+\end{forlines}
 \subinc{\input{../../global/epilogue}}

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_model_basics.tex

-                      r11693
+                      r14789
 \chapter{Model Basics}
 \label{chap:MB}
-\thispagestyle{plain}
 \chaptertoc
 …
 In this case, the free surface equation is nonlinear,
 and the variations of volume are fully taken into account.
 These coordinates systems is presented in a report \citep{levier.treguier.ea_rpt07} available on
+These coordinates systems is presented in a report \citep{levier.treguier.ea_trpt07} available on
 the \NEMO\ web site.
 …
 This problem can be at least partially overcome by mixing $s$-coordinate and
 step-like representation of bottom topography
 \citep{gerdes_JGR93*a,gerdes_JGR93*b,madec.delecluse.ea_JPO96}.
+\citep{gerdes_JGR93,gerdes_JGR93*a,madec.delecluse.ea_JPO96}.
 However, the definition of the model domain vertical coordinate becomes then a non-trivial thing for
 a realistic bottom topography:

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

-                      r11693
+                      r14789
 \chapter{ essai \zstar \sstar}
-\thispagestyle{plain}
 \chaptertoc
 …
 In that case, the free surface equation is nonlinear, and the variations of volume are fully taken into account.
 These coordinates systems is presented in a report \citep{levier.treguier.ea_rpt07} available on the \NEMO\ web site.
+These coordinates systems is presented in a report \citep{levier.treguier.ea_trpt07} available on the \NEMO\ web site.
 \colorbox{yellow}{  end of to be updated}
 …
 %\nlst{nam_dynspg}
 Options are defined through the \nam{_dynspg}{\_dynspg} namelist variables.
 The surface pressure gradient term is related to the representation of the free surface (\autoref{sec:MB_hor_pg}).
 …
 which imposes a very small time step when an explicit time stepping is used.
 Two methods are proposed to allow a longer time step for the three-dimensional equations:
 the filtered free surface, which is a modification of the continuous equations %(see \autoref{eq:MB_flt?}),
+the filtered free surface, which is a modification of the continuous equations \iffalse (see \autoref{eq:MB_flt?}) \fi ,
 and the split-explicit free surface described below.
 The extra term introduced in the filtered method is calculated implicitly,
 …
 The split-explicit formulation has a damping effect on external gravity waves,
 which is weaker than the filtered free surface but still significant as shown by \citet{levier.treguier.ea_rpt07} in
+which is weaker than the filtered free surface but still significant as shown by \citet{levier.treguier.ea_trpt07} in
 the case of an analytical barotropic Kelvin wave.
 …
 In the non-linear free surface formulation, the variations of volume are fully taken into account.
 This option is presented in a report \citep{levier.treguier.ea_rpt07} available on the \NEMO\ web site.
+This option is presented in a report \citep{levier.treguier.ea_trpt07} available on the \NEMO\ web site.
 The three time-stepping methods (explicit, split-explicit and filtered) are the same as in
 \autoref{?:DYN_spg_linear?} except that the ocean depth is now time-dependent.

NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_time_domain.tex

-                      r11693
+                      r14789
 \label{chap:TD}
-\thispagestyle{plain}
 \chaptertoc
 …
 {\footnotesize
   \begin{tabularx}{0.5\textwidth}{l||X|X}
     Release          & Author(s)                                       &
+    Release          & Author(s)                                       &
     Modifications                                                      \\
     \hline
     {\em        4.0} & {\em J\'{e}r\^{o}me Chanut \newline Tim Graham} &
+    {\em        4.0} & {\em J\'{e}r\^{o}me Chanut \newline Tim Graham} &
     {\em Review \newline Update                                      } \\
     {\em        3.6} & {\em Christian \'{E}th\'{e}                   } &
+    {\em        3.6} & {\em Christian \'{E}th\'{e}                   } &
     {\em Update                                                      } \\
     {\em $\leq$ 3.4} & {\em Gurvan Madec                             } &
+    {\em $\leq$ 3.4} & {\em Gurvan Madec                             } &
     {\em First version                                               } \\
   \end{tabularx}
 …
 The time stepping used in \NEMO\ is a three level scheme that can be represented as follows:
 \begin{equation}
   \label{eq:TD}
   x^{t + \rdt} = x^{t - \rdt} + 2 \, \rdt \ \text{RHS}_x^{t - \rdt, \, t, \, t + \rdt}
 \end{equation}
 where $x$ stands for $u$, $v$, $T$ or $S$;
 RHS is the \textbf{R}ight-\textbf{H}and-\textbf{S}ide of the corresponding time evolution equation;
 …
 first designed by \citet{robert_JMSJ66} and more comprehensively studied by \citet{asselin_MWR72},
 is a kind of laplacian diffusion in time that mixes odd and even time steps:
 \begin{equation}
   \label{eq:TD_asselin}
   x_F^t = x^t + \gamma \, \lt[ x_F^{t - \rdt} - 2 x^t + x^{t + \rdt} \rt]
 \end{equation}
 where the subscript $F$ denotes filtered values and $\gamma$ is the Asselin coefficient.
 $\gamma$ is initialized as \np{rn_atfp}{rn\_atfp} (namelist parameter).
 …
 The conditions for stability of second and fourth order horizontal diffusion schemes are
 \citep{griffies_bk04}:
 \begin{equation}
   \label{eq:TD_euler_stability}
 …
   \end{cases}
 \end{equation}
 where $e$ is the smallest grid size in the two horizontal directions and
 $A^h$ is the mixing coefficient.
 …
 To overcome the stability constraint, a backward (or implicit) time differencing scheme is used.
 This scheme is unconditionally stable but diffusive and can be written as follows:
 \begin{equation}
   \label{eq:TD_imp}
 …
 where RHS is the right hand side of the equation except for the vertical diffusion term.
 We rewrite \autoref{eq:TD_imp} as:
 \begin{equation}
   \label{eq:TD_imp_mat}
   -c(k + 1) \; T^{t + 1}(k + 1) + d(k) \; T^{t + 1}(k) - \; c(k) \; T^{t + 1}(k - 1) \equiv b(k)
 \end{equation}
 where
 \[
   c(k) = A_w^{vT} (k) \, / \, e_{3w} (k) \text{,} \quad
 …
 $Q$ is redistributed over several time step.
 In the modified LF-RA environment, these two formulations have been replaced by:
 \begin{gather}
   \label{eq:TD_forcing}
 …
                     - \gamma \, \rdt \, \lt( Q^{t + \rdt / 2} - Q^{t - \rdt / 2} \rt)
 \end{gather}
 The change in the forcing formulation given by \autoref{eq:TD_forcing}
 (see \autoref{fig:TD_MLF_forcing}) has a significant effect:
 …
+  %
 \end{flalign*}
 \begin{flalign*}
   \allowdisplaybreaks
 …
+  %
 \end{flalign*}
 \begin{flalign*}
   \allowdisplaybreaks

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