Changeset 11578

Timestamp:

2019-09-19T19:44:36+02:00 (5 years ago)

Author:

nicolasmartin

Message:

New LaTeX commands \nam and \np to mention namelist content (step 2)
So far so good, the manual compiles successfully 4 times and everything seems in its right place

Location:

NEMO/trunk/doc/latex/NEMO/subfiles

Files:

• apdx_DOMAINcfg.tex (modified) (9 diffs)
• chap_ASM.tex (modified) (2 diffs)
• chap_DIA.tex (modified) (10 diffs)
• chap_DIU.tex (modified) (1 diff)
• chap_DOM.tex (modified) (5 diffs)
• chap_DYN.tex (modified) (5 diffs)
• chap_LBC.tex (modified) (9 diffs)
• chap_LDF.tex (modified) (1 diff)
• chap_OBS.tex (modified) (6 diffs)
• chap_SBC.tex (modified) (9 diffs)
• chap_STO.tex (modified) (1 diff)
• chap_TRA.tex (modified) (6 diffs)
• chap_ZDF.tex (modified) (10 diffs)
• chap_cfgs.tex (modified) (3 diffs)
• chap_misc.tex (modified) (4 diffs)
• chap_model_basics_zstar.tex (modified) (2 diffs)
• chap_time_domain.tex (modified) (2 diffs)

NEMO/trunk/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex

@@ -51 +51 @@
 
 The user has three options available in defining a horizontal grid, which involve the
-namelist variable \np{jphgr_mesh}{jphgr\_mesh} of the \nam{dom} (\texttt{DOMAINcfg} variant only)
+namelist variable \np{jphgr_mesh}{jphgr\_mesh} of the \nam{dom}{dom} (\texttt{DOMAINcfg} variant only)
 namelist.
 
@@ -81 +81 @@
 In these two cases (\np{jphgr_mesh}{jphgr\_mesh}=1 or 4), the grid position is defined by the
 longitude and latitude of the south-westernmost point (\np{ppglamt0}
-and \np{ppgphi0}). Note that for the Mercator grid the user need only provide
+and \np{ppgphi0}{ppgphi0}). Note that for the Mercator grid the user need only provide
 an approximate starting latitude: the real latitude will be recalculated analytically,
 in order to ensure that the equator corresponds to line passing through $t$-
@@ -87 +87 @@
 
 Rectangular grids ignoring the spherical geometry are defined with
-\np{jphgr_mesh}{jphgr\_mesh} = 2, 3, 5. The domain is either an $f$-plane (\np{jphgr\_mesh} = 2,
+\np{jphgr_mesh}{jphgr\_mesh} = 2, 3, 5. The domain is either an $f$-plane (\np{jphgr_mesh}{jphgr\_mesh} = 2,
 Coriolis factor is constant) or a beta-plane (\np{jphgr_mesh}{jphgr\_mesh} = 3, the Coriolis factor
 is linear in the $j$-direction). The grid size is uniform in meter in each direction,
@@ -94 +94 @@
 with the first $t$-point. The meridional coordinate (gphi. arrays) is in kilometers,
 and the second $t$-point corresponds to coordinate $gphit=0$. The input
-variable \np{ppglam0} is ignored. \np{ppgphi0} is used to set the reference
+variable \np{ppglam0}{ppglam0} is ignored. \np{ppgphi0}{ppgphi0} is used to set the reference
 latitude for computation of the Coriolis parameter. In the case of the beta plane,
-\np{ppgphi0} corresponds to the center of the domain. Finally, the special case
+\np{ppgphi0}{ppgphi0} corresponds to the center of the domain. Finally, the special case
 \np{jphgr_mesh}{jphgr\_mesh}=5 corresponds to a beta plane in a rotated domain for the
 GYRE configuration, representing a classical mid-latitude double gyre system.
@@ -132 +132 @@
 the vertical scale factors.  The user must provide the analytical expression of both $z_0$
 and its first derivative with respect to $k$.  This is done in routine \mdl{domzgr}
-through statement functions, using parameters provided in the \nam{dom} namelist
+through statement functions, using parameters provided in the \nam{dom}{dom} namelist
 (\texttt{DOMAINcfg} variant).
 
 It is possible to define a simple regular vertical grid by giving zero stretching
-(\np{ppacr}\forcode{ = 0}).  In that case, the parameters \jp{jpk} (number of $w$-levels)
-and \np{pphmax} (total ocean depth in meters) fully define the grid.
+(\np{ppacr}{ppacr}\forcode{ = 0}).  In that case, the parameters \jp{jpk} (number of $w$-levels)
+and \np{pphmax}{pphmax} (total ocean depth in meters) fully define the grid.
 
 For climate-related studies it is often desirable to concentrate the vertical resolution
@@ -152 +152 @@
 top and bottom with a smooth hyperbolic tangent transition in between (\autoref{fig:DOMCFG_zgr}).
 
-A double hyperbolic tangent version (\np{ldbletanh}\forcode{ = .true.}) is also available
+A double hyperbolic tangent version (\np{ldbletanh}{ldbletanh}\forcode{ = .true.}) is also available
 which permits finer control and is used, typically, to obtain a well resolved upper ocean
 without compromising on resolution at depth using a moderate number of levels.
@@ -204 +204 @@
 The resulting depths and scale factors as a function of the model levels are shown in
 \autoref{fig:DOMCFG_zgr} and given in \autoref{tab:DOMCFG_orca_zgr}.
-Those values correspond to the parameters \np{ppsur}, \np{ppa0}, \np{ppa1}, \np{ppkth} in \nam{cfg} namelist.
+Those values correspond to the parameters \np{ppsur}{ppsur}, \np{ppa0}{ppa0}, \np{ppa1}{ppa1}, \np{ppkth}{ppkth} in \nam{cfg}{cfg} namelist.
 
 Rather than entering parameters $h_{sur}$, $h_0$, and $h_1$ directly, it is possible to
-recalculate them.  In that case the user sets \np{ppsur}~$=$~\np{ppa0}~$=$~\np{ppa1}~$=
-999999$., in \nam{cfg} namelist, and specifies instead the four following parameters:
+recalculate them.  In that case the user sets \np{ppsur}{ppsur}~$=$~\np{ppa0}{ppa0}~$=$~\np{ppa1}{ppa1}~$=
+999999$., in \nam{cfg}{cfg} namelist, and specifies instead the four following parameters:
 \begin{itemize}
 \item
-  \np{ppacr}~$= h_{cr}$: stretching factor (nondimensional).
-  The larger \np{ppacr}, the smaller the stretching.
+  \np{ppacr}{ppacr}~$= h_{cr}$: stretching factor (nondimensional).
+  The larger \np{ppacr}{ppacr}, the smaller the stretching.
   Values from $3$ to $10$ are usual.
 \item
-  \np{ppkth}~$= h_{th}$: is approximately the model level at which maximum stretching occurs
+  \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})
 \item
-  \np{ppdzmin}: minimum thickness for the top layer (in meters).
+  \np{ppdzmin}{ppdzmin}: minimum thickness for the top layer (in meters).
 \item
-  \np{pphmax}: total depth of the ocean (meters).
+  \np{pphmax}{pphmax}: total depth of the ocean (meters).
 \end{itemize}
 
 As an example, for the $45$ layers used in the DRAKKAR configuration those parameters are:
-\jp{jpk}~$= 46$, \np{ppacr}~$= 9$, \np{ppkth}~$= 23.563$, \np{ppdzmin}~$= 6~m$,
-\np{pphmax}~$= 5750~m$.
+\jp{jpk}~$= 46$, \np{ppacr}{ppacr}~$= 9$, \np{ppkth}{ppkth}~$= 23.563$, \np{ppdzmin}{ppdzmin}~$= 6~m$,
+\np{pphmax}{pphmax}~$= 5750~m$.
 
 %% %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -312 +312 @@
 
 Three options are possible for defining the bathymetry, according to the namelist variable
-\np{nn_bathy}{nn\_bathy} (found in \nam{dom} namelist (\texttt{DOMAINCFG} variant) ):
+\np{nn_bathy}{nn\_bathy} (found in \nam{dom}{dom} namelist (\texttt{DOMAINCFG} variant) ):
 \begin{description}
 \item[\np{nn_bathy}{nn\_bathy}\forcode{ = 0}]:
   a flat-bottom domain is defined.
   The total depth $z_w (jpk)$ is given by the coordinate transformation.
-  The domain can either be a closed basin or a periodic channel depending on the parameter \np{jperio}.
+  The domain can either be a closed basin or a periodic channel depending on the parameter \np{jperio}{jperio}.
 \item[\np{nn_bathy}{nn\_bathy}\forcode{ = -1}]:
   a domain with a bump of topography one third of the domain width at the central latitude.
@@ -387 +387 @@
 thickness than $e_{3t}(jpk)$: the maximum thickness allowed is $2*e_{3t}(jpk - 1)$.
 
-This has to be kept in mind when specifying values in \nam{dom} namelist
-(\texttt{DOMAINCFG} variant), such as the maximum depth \np{pphmax} in partial steps.
-
-For example, with \np{pphmax}~$= 5750~m$ for the DRAKKAR 45 layer grid, the maximum ocean
+This has to be kept in mind when specifying values in \nam{dom}{dom} namelist
+(\texttt{DOMAINCFG} variant), such as the maximum depth \np{pphmax}{pphmax} in partial steps.
+
+For example, with \np{pphmax}{pphmax}~$= 5750~m$ for the DRAKKAR 45 layer grid, the maximum ocean
 depth allowed is actually $6000~m$ (the default thickness $e_{3t}(jpk - 1)$ being
 $250~m$).  Two variables in the namdom namelist are used to define the partial step

NEMO/trunk/doc/latex/NEMO/subfiles/chap_ASM.tex

@@ -64 +64 @@
 Typically the increments are spread evenly over the full window.
 In addition, two different weighting functions have been implemented.
-The first function (namelist option \np{niaufn}=0) employs constant weights,
+The first function (namelist option \np{niaufn}{niaufn}=0) employs constant weights,
 \begin{align}
   \label{eq:ASM_F1_i}
@@ -77 +77 @@
 \end{align}
 where $M = m-n$.
-The second function (namelist option \np{niaufn}=1) employs peaked hat-like weights in order to give maximum weight in the centre of the sub-window,
+The second function (namelist option \np{niaufn}{niaufn}=1) employs peaked hat-like weights in order to give maximum weight in the centre of the sub-window,
 with the weighting reduced linearly to a small value at the window end-points:
 \begin{align}

NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex

@@ -1323 +1323 @@
 
 Some metadata that may significantly increase the file size (horizontal cell areas and vertices) are controlled by
-the namelist parameter \np{ln_cfmeta}{ln\_cfmeta} in the \nam{run} namelist.
+the namelist parameter \np{ln_cfmeta}{ln\_cfmeta} in the \nam{run}{run} namelist.
 This must be set to true if these metadata are to be included in the output files.
 
@@ -1345 +1345 @@
 most analysis codes can be relinked simply with the new libraries and will then read both NetCDF3 and NetCDF4 files.
 \NEMO\ executables linked with NetCDF4 libraries can be made to produce NetCDF3 files by
-setting the \np{ln_nc4zip}{ln\_nc4zip} logical to false in the \nam{nc4} namelist:
+setting the \np{ln_nc4zip}{ln\_nc4zip} logical to false in the \nam{nc4}{nc4} namelist:
 
 %------------------------------------------namnc4----------------------------------------------------
@@ -1438 +1438 @@
 
 When \key{iomput} is activated with \key{netcdf4} chunking and compression parameters for fields produced via
-\rou{iom\_put} calls are set via an equivalent and identically named namelist to \nam{nc4} in
+\rou{iom\_put} calls are set via an equivalent and identically named namelist to \nam{nc4}{nc4} in
 \textit{xmlio\_server.def}.
-Typically this namelist serves the mean files whilst the \nam{nc4} in the main namelist file continues to
+Typically this namelist serves the mean files whilst the \nam{nc4}{nc4} in the main namelist file continues to
 serve the restart files.
 This duplication is unfortunate but appropriate since, if using io\_servers, the domain sizes of
@@ -1449 +1449 @@
 %       Tracer/Dynamics Trends
 % -------------------------------------------------------------------------------------------------------------
-\section[Tracer/Dynamics trends (\forcode{&namtrd})]{Tracer/Dynamics trends (\protect\nam{trd})}
+\section[Tracer/Dynamics trends (\forcode{&namtrd})]{Tracer/Dynamics trends (\protect\nam{trd}{trd})}
 \label{sec:DIA_trd}
 
@@ -1464 +1464 @@
 \mdl{trddyn} and/or \mdl{trdtra} modules (see TRD directory) just after their computation
 (\ie\ at the end of each \textit{dyn....F90} and/or \textit{tra....F90} routines).
-This capability is controlled by options offered in \nam{trd} namelist.
+This capability is controlled by options offered in \nam{trd}{trd} namelist.
 Note that the output are done with XIOS, and therefore the \key{iomput} is required.
 
-What is done depends on the \nam{trd} logical set to \forcode{.true.}:
+What is done depends on the \nam{trd}{trd} logical set to \forcode{.true.}:
 
 \begin{description}
@@ -1513 +1513 @@
 The on-line computation of floats advected either by the three dimensional velocity field or constraint to
 remain at a given depth ($w = 0$ in the computation) have been introduced in the system during the CLIPPER project.
-Options are defined by \nam{flo} namelist variables.
+Options are defined by \nam{flo}{flo} namelist variables.
 The algorithm used is based either on the work of \cite{blanke.raynaud_JPO97} (default option),
 or on a $4^th$ Runge-Hutta algorithm (\np{ln_flork4}{ln\_flork4}\forcode{=.true.}).
@@ -1572 +1572 @@
 } \\
 
-\np{jpnfl} is the total number of floats during the run.
+\np{jpnfl}{jpnfl} is the total number of floats during the run.
 When initial positions are read in a restart file (\np{ln_rstflo}{ln\_rstflo}\forcode{=.true.} ),
-\np{jpnflnewflo} can be added in the initialization file.
+\np{jpnflnewflo}{jpnflnewflo} can be added in the initialization file.
 
 \subsubsection{Output data}
@@ -1631 +1631 @@
 % - \np{nb_ana}{nb\_ana}     is the number of harmonics to analyse
 
- - \np{tname}       is an array with names of tidal constituents to analyse
-
- \np{nit000_han}{nit000\_han} and \np{nitend_han}{nitend\_han} must be between \np{nit000} and \np{nitend} of the simulation.
+ - \np{tname}{tname}       is an array with names of tidal constituents to analyse
+
+ \np{nit000_han}{nit000\_han} and \np{nitend_han}{nitend\_han} must be between \np{nit000}{nit000} and \np{nitend}{nitend} of the simulation.
  The restart capability is not implemented.
 
@@ -2035 +2035 @@
 
 In \mdl{diaptr} when \np{ln_diaptr}{ln\_diaptr}\forcode{=.true.}
-(see the \nam{ptr} namelist below) can be computed on-line the poleward heat and salt transports,
+(see the \nam{ptr}{ptr} namelist below) can be computed on-line the poleward heat and salt transports,
 their advective and diffusive component, and the meriodional stream function .
 When \np{ln_subbas}{ln\_subbas}\forcode{=.true.}, transports and stream function are computed for the Atlantic, Indian,
@@ -2109 +2109 @@
 Values greater than 1 indicate that information is propagated across more than one grid cell in a single time step.
 
-The variables can be activated by setting the \np{nn_diacfl}{nn\_diacfl} namelist parameter to 1 in the \nam{ctl} namelist.
+The variables can be activated by setting the \np{nn_diacfl}{nn\_diacfl} namelist parameter to 1 in the \nam{ctl}{ctl} namelist.
 The diagnostics will be written out to an ascii file named cfl\_diagnostics.ascii.
 In this file the maximum value of $C_u$, $C_v$, and $C_w$ are printed at each timestep along with the coordinates of

NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIU.tex

@@ -36 +36 @@
 both must be added to a foundation SST to obtain the true skin temperature.
 
-Both the cool skin and warm layer models are controlled through the namelist \nam{diu}:
+Both the cool skin and warm layer models are controlled through the namelist \nam{diu}{diu}:
 
 \begin{listing}

NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex

@@ -335 +335 @@
 
 Two typical methods are available to specify the spatial domain configuration;
-they can be selected using parameter \np{ln_read_cfg}{ln\_read\_cfg} parameter in namelist \nam{cfg}.
+they can be selected using parameter \np{ln_read_cfg}{ln\_read\_cfg} parameter in namelist \nam{cfg}{cfg}.
 
 If \np{ln_read_cfg}{ln\_read\_cfg} is set to \forcode{.true.},
 the domain-specific parameters and fields are read from a netCDF input file,
-whose name (without its .nc suffix) can be specified as the value of the \np{cn_domcfg}{cn\_domcfg} parameter in namelist \nam{cfg}.
+whose name (without its .nc suffix) can be specified as the value of the \np{cn_domcfg}{cn\_domcfg} parameter in namelist \nam{cfg}{cfg}.
 
 If \np{ln_read_cfg}{ln\_read\_cfg} is set to \forcode{.false.},
@@ -502 +502 @@
 a single configuration file can support both options.
 
-By default a non-linear free surface is used (\np{ln_linssh}{ln\_linssh} set to \forcode{=.false.} in \nam{dom}):
+By default a non-linear free surface is used (\np{ln_linssh}{ln\_linssh} set to \forcode{=.false.} in \nam{dom}{dom}):
 the coordinate follow the time-variation of the free surface so that the transformation is time dependent:
 $z(i,j,k,t)$ (\eg\ \autoref{fig:DOM_z_zps_s_sps}f).
-When a linear free surface is assumed (\np{ln_linssh}{ln\_linssh} set to \forcode{=.true.} in \nam{dom}),
+When a linear free surface is assumed (\np{ln_linssh}{ln\_linssh} set to \forcode{=.true.} in \nam{dom}{dom}),
 the vertical coordinates are fixed in time, but the seawater can move up and down across the $z_0$ surface
 (in other words, the top of the ocean in not a rigid lid).
@@ -652 +652 @@
 (grid-point position, scale factors)
 can be saved in a file if
-namelist parameter \np{ln_write_cfg}{ln\_write\_cfg} (namelist \nam{cfg}) is set to \forcode{.true.};
+namelist parameter \np{ln_write_cfg}{ln\_write\_cfg} (namelist \nam{cfg}{cfg}) is set to \forcode{.true.};
 the output filename is set through parameter \np{cn_domcfg_out}{cn\_domcfg\_out}.
 This is only really useful if
@@ -661 +661 @@
 (grid-point position, scale factors, depths and masks)
 can be saved in a file called \texttt{mesh\_mask} if
-namelist parameter \np{ln_meshmask}{ln\_meshmask} (namelist \nam{dom}) is set to \forcode{.true.}.
+namelist parameter \np{ln_meshmask}{ln\_meshmask} (namelist \nam{dom}{dom}) is set to \forcode{.true.}.
 This file contains additional fields that can be useful for post-processing applications.
 
@@ -677 +677 @@
 %------------------------------------------------------------------------------------------
 
-Basic initial state options are defined in \nam{tsd}.
+Basic initial state options are defined in \nam{tsd}{tsd}.
 By default, the ocean starts from rest (the velocity field is set to zero) and
 the initialization of temperature and salinity fields is controlled through the \np{ln_tsd_init}{ln\_tsd\_init} namelist parameter.

NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex

@@ -327 +327 @@
 A key point in \autoref{eq:DYN_een_e3f} is how the averaging in the \textbf{i}- and \textbf{j}- directions is made.
 It uses the sum of masked t-point vertical scale factor divided either by the sum of the four t-point masks
-(\np{nn_een_e3f}{nn\_een\_e3f}\forcode{=1}), or just by $4$ (\np{nn\_een\_e3f}\forcode{=.true.}).
+(\np{nn_een_e3f}{nn\_een\_e3f}\forcode{=1}), or just by $4$ (\np{nn_een_e3f}{nn\_een\_e3f}\forcode{=.true.}).
 The latter case preserves the continuity of $e_{3f}$ when one or more of the neighbouring $e_{3t}$ tends to zero and
 extends by continuity the value of $e_{3f}$ into the land areas.
@@ -904 +904 @@
     In this particular exemple,
     a boxcar averaging window over \np{nn_baro}{nn\_baro} barotropic time steps is used
-    (\np{nn\_bt\_flt}\forcode{=1}) and \np{nn_baro}{nn\_baro}\forcode{=5}.
+    (\np{nn_bt_flt}{nn\_bt\_flt}\forcode{=1}) and \np{nn_baro}{nn\_baro}\forcode{=5}.
     Internal mode time steps (which are also the model time steps) are denoted by
     $t-\rdt$, $t$ and $t+\rdt$.
@@ -1265 +1265 @@
 %-------------------------------------------------------------------------------------------------------------
 
-Options are defined through the \nam{zdf} namelist variables.
+Options are defined through the \nam{zdf}{zdf} namelist variables.
 The large vertical diffusion coefficient found in the surface mixed layer together with high vertical resolution implies that in the case of explicit time stepping there would be too restrictive a constraint on the time step.
 Two time stepping schemes can be used for the vertical diffusion term:
@@ -1409 +1409 @@
 flux is from a cell with water depth greater than \np{rn_wdmin1}{rn\_wdmin1} and 0 otherwise. If the user sets
 \np{ln_wd_dl_ramp}{ln\_wd\_dl\_ramp}\forcode{=.true.} the flux across the face is ramped down as the water depth decreases
-from 2 * \np{rn_wdmin1}{rn\_wdmin1} to \np{rn\_wdmin1}. The use of this ramp reduced grid-scale noise in idealised test cases.
+from 2 * \np{rn_wdmin1}{rn\_wdmin1} to \np{rn_wdmin1}{rn\_wdmin1}. The use of this ramp reduced grid-scale noise in idealised test cases.
 
 At the point where the flux across a $u$-face is multiplied by zuwdmask , we have chosen
@@ -1649 +1649 @@
 %-------------------------------------------------------------------------------------------------------------
 
-Options are defined through the \nam{dom} namelist variables.
+Options are defined through the \nam{dom}{dom} namelist variables.
 The general framework for dynamics time stepping is a leap-frog scheme,
 \ie\ a three level centred time scheme associated with an Asselin time filter (cf. \autoref{chap:TD}).

NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex

@@ -43 +43 @@
 %The process of defining which areas are to be masked is described in \autoref{subsec:DOM_msk}.
 
-Options are defined through the \nam{lbc} namelist variables.
+Options are defined through the \nam{lbc}{lbc} namelist variables.
 The discrete representation of a domain with complex boundaries (coastlines and bottom topography) leads to
 arrays that include large portions where a computation is not required as the model variables remain at zero.
@@ -173 +173 @@
 
 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}.
+setting \jp{jperio} to 0, 1, 2 or 7 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 $j=jpj-1$,
@@ -296 +296 @@
 The total number of subdomains corresponds to the number of MPI processes allocated to \NEMO\ when the model is launched
 (\ie\ mpirun -np x ./nemo will automatically give x subdomains).
-The i-axis is divided by \np{jpni} and the j-axis by \np{jpnj}.
-These parameters are defined in \nam{mpp} namelist.
-If \np{jpni} and \np{jpnj} are < 1, they will be automatically redefined in the code to give the best domain decomposition
+The i-axis is divided by \np{jpni}{jpni} and the j-axis by \np{jpnj}{jpnj}.
+These parameters are defined in \nam{mpp}{mpp} namelist.
+If \np{jpni}{jpni} and \np{jpnj}{jpnj} are < 1, they will be automatically redefined in the code to give the best domain decomposition
 (see bellow).
 
@@ -330 +330 @@
   N_{mpi} = jpni \times jpnj - N_{land} + N_{useless}
 \]
-$N_{land}$ is the total number of land subdomains in the domain decomposition defined by \np{jpni} and \np{jpnj}. $N_{useless}$ is the number of land subdomains that are kept in the compuational domain in order to make sure that $N_{mpi}$ MPI processes are indeed allocated to a given subdomain. The values of $N_{mpi}$, \np{jpni}, \np{jpnj},  $N_{land}$ and $N_{useless}$ are printed in the output file \texttt{ocean.output}. $N_{useless}$ must, of course, be as small as possible to limit the waste of ressources. A warning is issued in  \texttt{ocean.output} if $N_{useless}$ is not zero. Note that non-zero value of $N_{useless}$ is uselly required when using AGRIF as, up to now, the parent grid and each of the child grids must use all the $N_{mpi}$ processes.
-
-If the domain decomposition is automatically defined (when \np{jpni} and \np{jpnj} are < 1), the decomposition chosen by the model will minimise the sub-domain size (defined as $max_{all domains}(jpi \times jpj)$) and maximize the number of eliminated land subdomains. This means that no other domain decomposition (a set of \np{jpni} and \np{jpnj} values) will use less processes than $(jpni  \times  jpnj - N_{land})$ and get a smaller subdomain size.
-In order to specify $N_{mpi}$ properly (minimize $N_{useless}$), you must run the model once with \np{ln_list}{ln\_list} activated. In this case, the model will start the initialisation phase, print the list of optimum decompositions ($N_{mpi}$, \np{jpni} and \np{jpnj}) in \texttt{ocean.output} and directly abort. The maximum value of $N_{mpi}$ tested in this list is given by $max(N_{MPI\_tasks}, jpni \times jpnj)$. For example, run the model on 40 nodes with ln\_list activated and $jpni = 10000$ and $jpnj = 1$, will print the list of optimum domains decomposition from 1 to about 10000.
-
-Processors are numbered from 0 to $N_{mpi} - 1$. Subdomains containning some ocean points are numbered first from 0 to $jpni * jpnj - N_{land} -1$. The remaining $N_{useless}$ land subdomains are numbered next, which means that, for a given (\np{jpni}, \np{jpnj}), the numbers attributed to he ocean subdomains do not vary with $N_{useless}$.
+$N_{land}$ is the total number of land subdomains in the domain decomposition defined by \np{jpni}{jpni} and \np{jpnj}{jpnj}. $N_{useless}$ is the number of land subdomains that are kept in the compuational domain in order to make sure that $N_{mpi}$ MPI processes are indeed allocated to a given subdomain. The values of $N_{mpi}$, \np{jpni}{jpni}, \np{jpnj}{jpnj},  $N_{land}$ and $N_{useless}$ are printed in the output file \texttt{ocean.output}. $N_{useless}$ must, of course, be as small as possible to limit the waste of ressources. A warning is issued in  \texttt{ocean.output} if $N_{useless}$ is not zero. Note that non-zero value of $N_{useless}$ is uselly required when using AGRIF as, up to now, the parent grid and each of the child grids must use all the $N_{mpi}$ processes.
+
+If the domain decomposition is automatically defined (when \np{jpni}{jpni} and \np{jpnj}{jpnj} are < 1), the decomposition chosen by the model will minimise the sub-domain size (defined as $max_{all domains}(jpi \times jpj)$) and maximize the number of eliminated land subdomains. This means that no other domain decomposition (a set of \np{jpni}{jpni} and \np{jpnj}{jpnj} values) will use less processes than $(jpni  \times  jpnj - N_{land})$ and get a smaller subdomain size.
+In order to specify $N_{mpi}$ properly (minimize $N_{useless}$), you must run the model once with \np{ln_list}{ln\_list} activated. In this case, the model will start the initialisation phase, print the list of optimum decompositions ($N_{mpi}$, \np{jpni}{jpni} and \np{jpnj}{jpnj}) in \texttt{ocean.output} and directly abort. The maximum value of $N_{mpi}$ tested in this list is given by $max(N_{MPI\_tasks}, jpni \times jpnj)$. For example, run the model on 40 nodes with ln\_list activated and $jpni = 10000$ and $jpnj = 1$, will print the list of optimum domains decomposition from 1 to about 10000.
+
+Processors are numbered from 0 to $N_{mpi} - 1$. Subdomains containning some ocean points are numbered first from 0 to $jpni * jpnj - N_{land} -1$. The remaining $N_{useless}$ land subdomains are numbered next, which means that, for a given (\np{jpni}{jpni}, \np{jpnj}{jpnj}), the numbers attributed to he ocean subdomains do not vary with $N_{useless}$.
 
 When land processors are eliminated, the value corresponding to these locations in the model output files is undefined. \np{ln_mskland}{ln\_mskland} must be activated in order avoid Not a Number values in output files. Note that it is better to not eliminate land processors when creating a meshmask file (\ie\ when setting a non-zero value to \np{nn_msh}{nn\_msh}).
@@ -378 +378 @@
 %-----------------------------------------------------------------------------------------------
 
-Options are defined through the \nam{bdy} and \nam{bdy_dta}{bdy\_dta} namelist variables.
+Options are defined through the \nam{bdy}{bdy} and \nam{bdy_dta}{bdy\_dta} namelist variables.
 The BDY module is the core implementation of open boundary conditions for regional configurations on
 ocean temperature, salinity, barotropic-baroclinic velocities, ice-snow concentration, thicknesses, temperatures, salinity and melt ponds concentration and thickness.
@@ -397 +397 @@
 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{ln_coords_file}{ln\_coords\_file}\forcode{=.false.}, and a namelist block \nam{bdy_index}{bdy\_index} must be included for each set) or read in from a file (\np{ln\_coords\_file}\forcode{=.true.}, and a ``\ifile{coordinates.bdy}'' file must be provided).
+(\np{ln_coords_file}{ln\_coords\_file}\forcode{=.false.}, and a namelist block \nam{bdy_index}{bdy\_index} must be included for each set) or read in from a file (\np{ln_coords_file}{ln\_coords\_file}\forcode{=.true.}, and a ``\ifile{coordinates.bdy}'' file must be provided).
 The coordinates.bdy file is analagous to the usual \NEMO\ ``\ifile{coordinates}'' file.
 In the example above, there are two boundary sets, the first of which is defined via a file and
@@ -422 +422 @@
 
 The boundary data is either set to initial conditions
-(\np{nn_tra_dta}{nn\_tra\_dta}\forcode{=0}) or forced with external data from a file (\np{nn\_tra\_dta}\forcode{=1}).
+(\np{nn_tra_dta}{nn\_tra\_dta}\forcode{=0}) or forced with external data from a file (\np{nn_tra_dta}{nn\_tra\_dta}\forcode{=1}).
 In case the 3d velocity data contain the total velocity (ie, baroclinic and barotropic velocity),
 the bdy code can derived baroclinic and barotropic velocities by setting \np{ln_full_vel}{ln\_full\_vel}\forcode{=.true.}
 For the barotropic solution there is also the option to use tidal harmonic forcing either by
-itself (\np{nn_dyn2d_dta}{nn\_dyn2d\_dta}\forcode{=2}) or in addition to other external data (\np{nn\_dyn2d\_dta}\forcode{=3}).\\
+itself (\np{nn_dyn2d_dta}{nn\_dyn2d\_dta}\forcode{=2}) or in addition to other external data (\np{nn_dyn2d_dta}{nn\_dyn2d\_dta}\forcode{=3}).\\
 If not set to initial conditions, sea-ice salinity, temperatures and melt ponds data at the boundary can either be read in a file or defined as constant (by \np{rn_ice_sal}{rn\_ice\_sal}, \np{rn_ice_tem}{rn\_ice\_tem}, \np{rn_ice_apnd}{rn\_ice\_apnd}, \np{rn_ice_hpnd}{rn\_ice\_hpnd}). Ice age is constant and defined by \np{rn_ice_age}{rn\_ice\_age}.
 
@@ -700 +700 @@
 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} array; see
+including their names in the \np{clname}{clname} array; see
 \autoref{sec:SBC_tide}). Specific options related to the reading in of
 the complex harmonic amplitudes of elevation (SSH) and barotropic
@@ -715 +715 @@
 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} with suffix
+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} with suffix \ifile{\_grid\_U}, and
+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} with suffix
+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} with suffix
+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} with suffix \ifile{tcname\_grid\_U}, and variables
+\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} with suffix
+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

NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex

@@ -332 +332 @@
 decreases linearly to $A^l$~= 2.10$^3$ m$^2$/s at the equator \citep{madec.delecluse.ea_JPO96, delecluse.madec_icol99}.
 Similar modified horizontal variations can be found with the Antarctic or Arctic sub-domain options of ORCA2 and ORCA05.
-The provided fields can either be 2d (\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=-20}, \np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=-20}) or 3d (\np{nn\_aht\_ijk\_t}\forcode{=-30},  \np{nn\_ahm\_ijk\_t}\forcode{=-30}). They must be given at U, V points for tracers and T, F points for momentum (see \autoref{tab:LDF_files}).
+The provided fields can either be 2d (\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=-20}, \np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=-20}) or 3d (\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=-30},  \np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=-30}). They must be given at U, V points for tracers and T, F points for momentum (see \autoref{tab:LDF_files}).
 
 %-------------------------------------------------TABLE---------------------------------------------------

NEMO/trunk/doc/latex/NEMO/subfiles/chap_OBS.tex

@@ -32 +32 @@
 The OBS code is called from \mdl{nemogcm} for model initialisation and to calculate the model equivalent values for observations on the 0th time step.
 The code is then called again after each time step from \mdl{step}.
-The code is only activated if the \nam{obs} namelist logical \np{ln_diaobs}{ln\_diaobs} is set to true.
+The code is only activated if the \nam{obs}{obs} namelist logical \np{ln_diaobs}{ln\_diaobs} is set to true.
 
 For all data types a 2D horizontal interpolator or averager is needed to
@@ -48 +48 @@
 Otherwise (by default) the model value from the nearest time step to the observation time is used.
 
-The code is controlled by the namelist \nam{obs}.
+The code is controlled by the namelist \nam{obs}{obs}.
 See the following sections for more details on setting up the namelist.
 
@@ -92 +92 @@
 \end{enumerate}
 
-Options are defined through the \nam{obs} namelist variables.
+Options are defined through the \nam{obs}{obs} namelist variables.
 The options \np{ln_t3d}{ln\_t3d} and \np{ln_s3d}{ln\_s3d} switch on the temperature and salinity profile observation operator code.
 The filename or array of filenames are specified using the \np{cn_profbfiles}{cn\_profbfiles} variable.
@@ -114 +114 @@
 \label{sec:OBS_details}
 
-Here we show a more complete example namelist \nam{obs} and also show the NetCDF headers of
+Here we show a more complete example namelist \nam{obs}{obs} and also show the NetCDF headers of
 the observation files that may be used with the observation operator.
 
@@ -896 +896 @@
 %--------------------------------------------------------------------------------------------------------
 \subsection{Configuring the standalone observation operator}
-The observation files and settings understood by \nam{obs} have been outlined in the online observation operator section.
-In addition is a further namelist \nam{sao} which used to set the input model fields for the SAO
+The observation files and settings understood by \nam{obs}{obs} have been outlined in the online observation operator section.
+In addition is a further namelist \nam{sao}{sao} which used to set the input model fields for the SAO
 
 \subsubsection{Single field}
@@ -907 +907 @@
 \textbf{votemper}, \textbf{vosaline} and optionally \textbf{sshn} present.
 
-For each field read there must be an entry in the \nam{sao} namelist specifying
+For each field read there must be an entry in the \nam{sao}{sao} namelist specifying
 the name of the file to read and the index along the \emph{time\_counter}.
 For example, to read the second time counter from a single file the namelist would be.

NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex

@@ -37 +37 @@
 
 Four different ways are available to provide the seven fields to the ocean. They are controlled by
-namelist \nam{sbc} variables:
+namelist \nam{sbc}{sbc} variables:
 
 \begin{itemize}
@@ -842 +842 @@
 
 The optional atmospheric pressure can be used to force ocean and ice dynamics
-(\np{ln_apr_dyn}{ln\_apr\_dyn}\forcode{=.true.}, \nam{sbc} namelist).
+(\np{ln_apr_dyn}{ln\_apr\_dyn}\forcode{=.true.}, \nam{sbc}{sbc} namelist).
 The input atmospheric forcing defined via \np{sn_apr}{sn\_apr} structure (\nam{sbc_apr}{sbc\_apr} namelist)
 can be interpolated in time to the model time step, and even in space when the interpolation on-the-fly is used.
@@ -1070 +1070 @@
 %--------------------------------------------------------------------------------------------------------
 
-The namelist variable in \nam{sbc}, \np{nn_isf}{nn\_isf}, controls the ice shelf representation.
+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}.
@@ -1266 +1266 @@
 (Note that the authors kindly provided a copy of their code to act as a basis for implementation in \NEMO).
 Icebergs are initially spawned into one of ten classes which have specific mass and thickness as
-described in the \nam{berg} namelist: \np{rn_initial_mass}{rn\_initial\_mass} and \np{rn_initial_thickness}{rn\_initial\_thickness}.
+described in the \nam{berg}{berg} namelist: \np{rn_initial_mass}{rn\_initial\_mass} and \np{rn_initial_thickness}{rn\_initial\_thickness}.
 Each class has an associated scaling (\np{rn_mass_scaling}{rn\_mass\_scaling}),
 which is an integer representing how many icebergs of this class are being described as one lagrangian point
@@ -1343 +1343 @@
 
 Physical processes related to ocean surface waves can be accounted by setting the logical variable
-\np{ln_wave}{ln\_wave}\forcode{=.true.} in \nam{sbc} namelist. In addition, specific flags accounting for
+\np{ln_wave}{ln\_wave}\forcode{=.true.} in \nam{sbc}{sbc} namelist. In addition, specific flags accounting for
 different processes should be activated as explained in the following sections.
 
@@ -1352 +1352 @@
 Input Data generic Interface (see \autoref{sec:SBC_input}).
 \item[coupled mode]: \NEMO\ and an external wave model can be coupled by setting \np{ln_cpl}{ln\_cpl} \forcode{= .true.}
-in \nam{sbc} namelist and filling the \nam{sbc_cpl}{sbc\_cpl} namelist.
+in \nam{sbc}{sbc} namelist and filling the \nam{sbc_cpl}{sbc\_cpl} namelist.
 \end{description}
 
@@ -1364 +1364 @@
 
 The neutral surface drag coefficient provided from an external data source (\ie\ a wave model),
-can be used by setting the logical variable \np{ln_cdgw}{ln\_cdgw} \forcode{= .true.} in \nam{sbc} namelist.
+can be used by setting the logical variable \np{ln_cdgw}{ln\_cdgw} \forcode{= .true.} in \nam{sbc}{sbc} namelist.
 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
@@ -1561 +1561 @@
 assuming that the diurnal cycle of SWF is a scaling of the top of the atmosphere diurnal cycle of incident SWF.
 The \cite{bernie.guilyardi.ea_CD07} reconstruction algorithm is available in \NEMO\ by
-setting \np{ln_dm2dc}{ln\_dm2dc}\forcode{=.true.} (a \textit{\nam{sbc}} namelist variable) when
+setting \np{ln_dm2dc}{ln\_dm2dc}\forcode{=.true.} (a \textit{\nam{sbc}{sbc}} namelist variable) when
 using a bulk formulation (\np{ln_blk}{ln\_blk}\forcode{=.true.}) or
 the flux formulation (\np{ln_flx}{ln\_flx}\forcode{=.true.}).
@@ -1668 +1668 @@
 The presence at the sea surface of an ice covered area modifies all the fluxes transmitted to the ocean.
 There are several way to handle sea-ice in the system depending on
-the value of the \np{nn_ice}{nn\_ice} namelist parameter found in \nam{sbc} namelist.
+the value of the \np{nn_ice}{nn\_ice} namelist parameter found in \nam{sbc}{sbc} namelist.
 \begin{description}
 \item[nn\_ice = 0]

NEMO/trunk/doc/latex/NEMO/subfiles/chap_STO.tex

@@ -172 +172 @@
 The \np{ln_sto_eos}{ln\_sto\_eos} namelist variable activates stochastic parametrisation of equation of state.
 By default it set to \forcode{.false.}) and not active.
-The set of parameters is available in \nam{sto} namelist
+The set of parameters is available in \nam{sto}{sto} namelist
 (only the subset for equation of state stochastic parametrisation is listed below):
 %---------------------------------------namsto--------------------------------------------------

NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex

@@ -635 +635 @@
 %--------------------------------------------------------------------------------------------------------------
 
-Options are defined through the \nam{zdf} namelist variables.
+Options are defined through the \nam{zdf}{zdf} namelist variables.
 The formulation of the vertical subgrid scale tracer physics is the same for all the vertical coordinates,
 and is based on a laplacian operator.
@@ -898 +898 @@
 (\ie\ the one associated with the Antarctic Bottom Water) by a few Sverdrups \citep{emile-geay.madec_OS09}.
 
-Options are defined through the \nam{bbc} namelist variables.
+Options are defined through the \nam{bbc}{bbc} namelist variables.
 The presence of geothermal heating is controlled by setting the namelist parameter \np{ln_trabbc}{ln\_trabbc} to true.
 Then, when \np{nn_geoflx}{nn\_geoflx} is set to 1, a constant geothermal heating is introduced whose value is given by
@@ -919 +919 @@
 %--------------------------------------------------------------------------------------------------------------
 
-Options are defined through the \nam{bbl} namelist variables.
+Options are defined through the \nam{bbl}{bbl} namelist variables.
 In a $z$-coordinate configuration, the bottom topography is represented by a series of discrete steps.
 This is not adequate to represent gravity driven downslope flows.
@@ -1098 +1098 @@
 The restoring term is added when the namelist parameter \np{ln_tradmp}{ln\_tradmp} is set to true.
 It also requires that both \np{ln_tsd_init}{ln\_tsd\_init} and \np{ln_tsd_dmp}{ln\_tsd\_dmp} are set to true in
-\nam{tsd} namelist as well as \np{sn_tem}{sn\_tem} and \np{sn_sal}{sn\_sal} structures are correctly set
+\nam{tsd}{tsd} namelist as well as \np{sn_tem}{sn\_tem} and \np{sn_sal}{sn\_sal} structures are correctly set
 (\ie\ that $T_o$ and $S_o$ are provided in input files and read using \mdl{fldread},
 see \autoref{subsec:SBC_fldread}).
@@ -1138 +1138 @@
 %--------------------------------------------------------------------------------------------------------------
 
-Options are defined through the \nam{dom} namelist variables.
+Options are defined through the \nam{dom}{dom} namelist variables.
 The general framework for tracer time stepping is a modified leap-frog scheme \citep{leclair.madec_OM09},
 \ie\ a three level centred time scheme associated with a Asselin time filter (cf. \autoref{sec:TD_mLF}):
@@ -1213 +1213 @@
 density in the World Ocean varies by no more than 2$\%$ from that value \citep{gill_bk82}.
 
-Options which control the EOS used are defined through the \nam{eos} namelist variables.
+Options which control the EOS used are defined through the \nam{eos}{eos} namelist variables.
 
 \begin{description}

NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex

@@ -61 +61 @@
 \label{subsec:ZDF_cst}
 
-Options are defined through the \nam{zdf} namelist variables.
+Options are defined through the \nam{zdf}{zdf} namelist variables.
 When \np{ln_zdfcst}{ln\_zdfcst} is defined, the momentum and tracer vertical eddy coefficients are set to
 constant values over the whole ocean.
@@ -211 +211 @@
 too weak vertical diffusion.
 They must be specified at least larger than the molecular values, and are set through \np{rn_avm0}{rn\_avm0} and
-\np{rn_avt0}{rn\_avt0} (\nam{zdf} namelist, see \autoref{subsec:ZDF_cst}).
+\np{rn_avt0}{rn\_avt0} (\nam{zdf}{zdf} namelist, see \autoref{subsec:ZDF_cst}).
 
 \subsubsection{Turbulent length scale}
@@ -225 +225 @@
 which is valid in a stable stratified region with constant values of the Brunt-Vais\"{a}l\"{a} frequency.
 The resulting length scale is bounded by the distance to the surface or to the bottom
-(\np{nn_mxl}{nn\_mxl}\forcode{=0}) or by the local vertical scale factor (\np{nn\_mxl}\forcode{=1}).
+(\np{nn_mxl}{nn\_mxl}\forcode{=0}) or by the local vertical scale factor (\np{nn_mxl}{nn\_mxl}\forcode{=1}).
 \citet{blanke.delecluse_JPO93} notice that this simplification has two major drawbacks:
 it makes no sense for locally unstable stratification and the computation no longer uses all
@@ -312 +312 @@
 $\alpha_{CB} = 100$ the Craig and Banner's value.
 As the surface boundary condition on TKE is prescribed through $\bar{e}_o = e_{bb} |\tau| / \rho_o$,
-with $e_{bb}$ the \np{rn_ebb}{rn\_ebb} namelist parameter, setting \np{rn\_ebb}\forcode{ = 67.83} corresponds
+with $e_{bb}$ the \np{rn_ebb}{rn\_ebb} namelist parameter, setting \np{rn_ebb}{rn\_ebb}\forcode{ = 67.83} corresponds
 to $\alpha_{CB} = 100$.
 Further setting  \np{ln_mxl0}{ln\_mxl0}\forcode{ =.true.},  applies \autoref{eq:ZDF_Lsbc} as the surface boundary condition on the length scale,
@@ -706 +706 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
-Options are defined through the \nam{zdf} namelist variables.
+Options are defined through the \nam{zdf}{zdf} namelist variables.
 The non-penetrative convective adjustment is used when \np{ln_zdfnpc}{ln\_zdfnpc}\forcode{=.true.}.
 It is applied at each \np{nn_npc}{nn\_npc} time step and mixes downwards instantaneously the statically unstable portion of
@@ -750 +750 @@
 \label{subsec:ZDF_evd}
 
-Options are defined through the  \nam{zdf} namelist variables.
+Options are defined through the  \nam{zdf}{zdf} namelist variables.
 The enhanced vertical diffusion parameterisation is used when \np{ln_zdfevd}{ln\_zdfevd}\forcode{=.true.}.
 In this case, the vertical eddy mixing coefficients are assigned very large values
@@ -811 +811 @@
 
 This parameterisation has been introduced in \mdl{zdfddm} module and is controlled by the namelist parameter
-\np{ln_zdfddm}{ln\_zdfddm} in \nam{zdf}.
+\np{ln_zdfddm}{ln\_zdfddm} in \nam{zdf}{zdf}.
 Double diffusion occurs when relatively warm, salty water overlies cooler, fresher water, or vice versa.
 The former condition leads to salt fingering and the latter to diffusive convection.
@@ -919 +919 @@
 %--------------------------------------------------------------------------------------------------------------
 
-Options to define the top and bottom friction are defined through the \nam{drg} namelist variables.
+Options to define the top and bottom friction are defined through the \nam{drg}{drg} namelist variables.
 The bottom friction represents the friction generated by the bathymetry.
 The top friction represents the friction generated by the ice shelf/ocean interface.
@@ -1142 +1142 @@
 An optional implicit form of bottom friction has been implemented to improve model stability.
 We recommend this option for shelf sea and coastal ocean applications. %, especially for split-explicit time splitting.
-This option can be invoked by setting \np{ln_drgimp}{ln\_drgimp} to \forcode{.true.} in the \nam{drg} namelist.
-%This option requires \np{ln_zdfexp}{ln\_zdfexp} to be \forcode{.false.} in the \nam{zdf} namelist.
+This option can be invoked by setting \np{ln_drgimp}{ln\_drgimp} to \forcode{.true.} in the \nam{drg}{drg} namelist.
+%This option requires \np{ln_zdfexp}{ln\_zdfexp} to be \forcode{.false.} in the \nam{zdf}{zdf} namelist.
 
 This implementation is performed in \mdl{dynzdf} where the following boundary conditions are set while solving the fully implicit diffusion step:
@@ -1170 +1170 @@
 \label{subsec:ZDF_drg_ts}
 
-With split-explicit free surface, the sub-stepping of barotropic equations needs the knowledge of top/bottom stresses. An obvious way to satisfy this is to take them as constant over the course of the barotropic integration and equal to the value used to update the baroclinic momentum trend. Provided \np{ln_drgimp}{ln\_drgimp}\forcode{= .false.} and a centred or \textit{leap-frog} like integration of barotropic equations is used (\ie\ \forcode{ln_bt_fw=.false.}, cf \autoref{subsec:DYN_spg_ts}), this does ensure that barotropic and baroclinic dynamics feel the same stresses during one leapfrog time step. However, if \np{ln\_drgimp}\forcode{= .true.},  stresses depend on the \textit{after} value of the velocities which themselves depend on the barotropic iteration result. This cyclic dependency makes difficult obtaining consistent stresses in 2d and 3d dynamics. Part of this mismatch is then removed when setting the final barotropic component of 3d velocities to the time splitting estimate. This last step can be seen as a necessary evil but should be minimized since it interferes with the adjustment to the boundary conditions.
+With split-explicit free surface, the sub-stepping of barotropic equations needs the knowledge of top/bottom stresses. An obvious way to satisfy this is to take them as constant over the course of the barotropic integration and equal to the value used to update the baroclinic momentum trend. Provided \np{ln_drgimp}{ln\_drgimp}\forcode{= .false.} and a centred or \textit{leap-frog} like integration of barotropic equations is used (\ie\ \forcode{ln_bt_fw=.false.}, cf \autoref{subsec:DYN_spg_ts}), this does ensure that barotropic and baroclinic dynamics feel the same stresses during one leapfrog time step. However, if \np{ln_drgimp}{ln\_drgimp}\forcode{= .true.},  stresses depend on the \textit{after} value of the velocities which themselves depend on the barotropic iteration result. This cyclic dependency makes difficult obtaining consistent stresses in 2d and 3d dynamics. Part of this mismatch is then removed when setting the final barotropic component of 3d velocities to the time splitting estimate. This last step can be seen as a necessary evil but should be minimized since it interferes with the adjustment to the boundary conditions.
 
 The strategy to handle top/bottom stresses with split-explicit free surface in \NEMO\ is as follows:

NEMO/trunk/doc/latex/NEMO/subfiles/chap_cfgs.tex

@@ -24 +24 @@
 The reference configurations also provide a sense for some of the options available in the code,
 though by no means are all options exercised in the reference configurations.
-Configuration is defined manually through the \nam{cfg} namelist variables.
+Configuration is defined manually through the \nam{cfg}{cfg} namelist variables.
 
 %------------------------------------------namcfg----------------------------------------------------
@@ -88 +88 @@
 https://doi.org/10.5281/zenodo.2640723
 
-In this namelist\_cfg the name of domain input file is set in \nam{cfg} block of namelist.
+In this namelist\_cfg the name of domain input file is set in \nam{cfg}{cfg} block of namelist.
 
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -253 +253 @@
 
 The GYRE configuration is set like an analytical configuration.
-Through \np{ln_read_cfg}{ln\_read\_cfg}\forcode{ = .false.} in \nam{cfg} namelist defined in
+Through \np{ln_read_cfg}{ln\_read\_cfg}\forcode{ = .false.} 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.

NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex

@@ -110 +110 @@
     \textit{Left}: a closea\_mask field;
     \textit{Right}: a closea\_mask\_rnf field.
-    In this example, if \protect\np{ln\_closea} is set to \forcode{.true.},
+    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
@@ -218 +218 @@
 \end{cmds}
 
-\item Add the logical switch \np{ln_use_jattr}{ln\_use\_jattr} to \nam{cfg} in the configuration
+\item Add the logical switch \np{ln_use_jattr}{ln\_use\_jattr} to \nam{cfg}{cfg} in the configuration
 namelist (if it is not already there) and set \forcode{.true.}
 \end{itemize}
@@ -331 +331 @@
 be set at all the locations actually required by each individual for the fold operation.
 This alternative method should give identical results to the default \textsc{ALLGATHER} method and
-is recommended for large values of \np{jpni}.
-The new method is activated by setting \np{ln_nnogather}{ln\_nnogather} to be true (\nam{mpp}).
+is recommended for large values of \np{jpni}{jpni}.
+The new method is activated by setting \np{ln_nnogather}{ln\_nnogather} to be true (\nam{mpp}{mpp}).
 The reproducibility of results using the two methods should be confirmed for each new,
 non-reference configuration.
@@ -350 +350 @@
 %--------------------------------------------------------------------------------------------------------------
 
-Options are defined through the  \nam{ctl} namelist variables.
+Options are defined through the  \nam{ctl}{ctl} namelist variables.
 
 \subsection{Vector optimisation}

NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

@@ -141 +141 @@
 The general idea is to solve the free surface equation with a small time step,
 while the three dimensional prognostic variables are solved with a longer time step that
-is a multiple of \np{rdtbt} in the \nam{dom} namelist (Figure III.3).
+is a multiple of \np{rdtbt}{rdtbt} in the \nam{dom}{dom} namelist (Figure III.3).
 
 %>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >
@@ -296 +296 @@
 The extra term introduced in the equations (see {\S}I.2.2) is solved implicitly.
 The elliptic solvers available in the code are documented in \autoref{chap:MISC}.
-The amplitude of the extra term is given by the namelist variable \np{rnu}.
+The amplitude of the extra term is given by the namelist variable \np{rnu}{rnu}.
 The default value is 1, as recommended by \citet{Roullet2000?}
 
-\colorbox{red}{\np{rnu}\forcode{=1} to be suppressed from namelist !}
+\colorbox{red}{\np{rnu}{rnu}\forcode{=1} to be suppressed from namelist !}
 
 %-------------------------------------------------------------

NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex

@@ -298 +298 @@
 is missing, an Euler time stepping scheme is imposed. A forward initial step can still be enforced by the user by setting
 the namelist variable \np{nn_euler}{nn\_euler}\forcode{=0}. Other options to control the time integration of the model
-are defined through the  \nam{run} namelist variables.
+are defined through the  \nam{run}{run} namelist variables.
 %%%
 \gmcomment{
@@ -322 +322 @@
 %--------------------------------------------------------------------------------------------------------------
 
-Options are defined through the  \nam{dom} namelist variables.
+Options are defined through the  \nam{dom}{dom} namelist variables.
  \colorbox{yellow}{add here a few word on nit000 and nitend}