Changeset 11582 for NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex

Timestamp:

2019-09-20T11:44:31+02:00 (5 years ago)

Author:

nicolasmartin

Message:

New LaTeX commands \nam and \np to mention namelist content (step 2)
Finally convert \forcode{...} following \np{}{} into optional arg of the new command \np[]{}{}

File:

• NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex (modified) (40 diffs)

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

@@ -1 +1 @@
 \documentclass[../main/NEMO_manual]{subfiles}
+
+\onlyinsubfile{\makeindex}
 
 \begin{document}
@@ -41 +43 @@
 \begin{itemize}
 \item
-  a bulk formulation (\np{ln_blk}{ln\_blk}\forcode{=.true.} with four possible bulk algorithms),
-\item
-  a flux formulation (\np{ln_flx}{ln\_flx}\forcode{=.true.}),
+  a bulk formulation (\np[=.true.]{ln_blk}{ln\_blk} with four possible bulk algorithms),
+\item
+  a flux formulation (\np[=.true.]{ln_flx}{ln\_flx}),
 \item
   a coupled or mixed forced/coupled formulation (exchanges with a atmospheric model via the OASIS coupler),
-(\np{ln_cpl}{ln\_cpl} or \np{ln_mixcpl}{ln\_mixcpl}\forcode{=.true.}),
-\item
-  a user defined formulation (\np{ln_usr}{ln\_usr}\forcode{=.true.}).
+(\np{ln_cpl}{ln\_cpl} or \np[=.true.]{ln_mixcpl}{ln\_mixcpl}),
+\item
+  a user defined formulation (\np[=.true.]{ln_usr}{ln\_usr}).
 \end{itemize}
 
@@ -69 +71 @@
   the local grid directions in the model,
 \item
-  the use of a land/sea mask for input fields (\np{nn_lsm}{nn\_lsm}\forcode{=.true.}),
-\item
-  the addition of a surface restoring term to observed SST and/or SSS (\np{ln_ssr}{ln\_ssr}\forcode{=.true.}),
+  the use of a land/sea mask for input fields (\np[=.true.]{nn_lsm}{nn\_lsm}),
+\item
+  the addition of a surface restoring term to observed SST and/or SSS (\np[=.true.]{ln_ssr}{ln\_ssr}),
 \item
   the modification of fluxes below ice-covered areas (using climatological ice-cover or a sea-ice model)
-  (\np{nn_ice}{nn\_ice}\forcode{=0..3}),
-\item
-  the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np{ln_rnf}{ln\_rnf}\forcode{=.true.}),
+  (\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{ln_isf}{ln\_isf}\forcode{=.true.}),
+  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{nn_fwb}{nn\_fwb}\forcode{=0..2}),
+  (\np[=0..2]{nn_fwb}{nn\_fwb}),
 \item
   the transformation of the solar radiation (if provided as daily mean) into an analytical diurnal cycle
-  (\np{ln_dm2dc}{ln\_dm2dc}\forcode{=.true.}),
-\item
-  the activation of wave effects from an external wave model  (\np{ln_wave}{ln\_wave}\forcode{=.true.}),
-\item
-  a neutral drag coefficient is read from an external wave model (\np{ln_cdgw}{ln\_cdgw}\forcode{=.true.}),
-\item
-  the Stokes drift from an external wave model is accounted for (\np{ln_sdw}{ln\_sdw}\forcode{=.true.}),
-\item
-  the choice of the Stokes drift profile parameterization (\np{nn_sdrift}{nn\_sdrift}\forcode{=0..2}),
-\item
-  the surface stress given to the ocean is modified by surface waves (\np{ln_tauwoc}{ln\_tauwoc}\forcode{=.true.}),
-\item
-  the surface stress given to the ocean is read from an external wave model (\np{ln_tauw}{ln\_tauw}\forcode{=.true.}),
-\item
-  the Stokes-Coriolis term is included (\np{ln_stcor}{ln\_stcor}\forcode{=.true.}),
-\item
-  the light penetration in the ocean (\np{ln_traqsr}{ln\_traqsr}\forcode{=.true.} with namelist \nam{tra_qsr}{tra\_qsr}),
-\item
-  the atmospheric surface pressure gradient effect on ocean and ice dynamics (\np{ln_apr_dyn}{ln\_apr\_dyn}\forcode{=.true.} with namelist \nam{sbc_apr}{sbc\_apr}),
-\item
-  the effect of sea-ice pressure on the ocean (\np{ln_ice_embd}{ln\_ice\_embd}\forcode{=.true.}).
+  (\np[=.true.]{ln_dm2dc}{ln\_dm2dc}),
+\item
+  the activation of wave effects from an external wave model  (\np[=.true.]{ln_wave}{ln\_wave}),
+\item
+  a neutral drag coefficient is read from an external wave model (\np[=.true.]{ln_cdgw}{ln\_cdgw}),
+\item
+  the Stokes drift from an external wave model is accounted for (\np[=.true.]{ln_sdw}{ln\_sdw}),
+\item
+  the choice of the Stokes drift profile parameterization (\np[=0..2]{nn_sdrift}{nn\_sdrift}),
+\item
+  the surface stress given to the ocean is modified by surface waves (\np[=.true.]{ln_tauwoc}{ln\_tauwoc}),
+\item
+  the surface stress given to the ocean is read from an external wave model (\np[=.true.]{ln_tauw}{ln\_tauw}),
+\item
+  the Stokes-Coriolis term is included (\np[=.true.]{ln_stcor}{ln\_stcor}),
+\item
+  the light penetration in the ocean (\np[=.true.]{ln_traqsr}{ln\_traqsr} with namelist \nam{tra_qsr}{tra\_qsr}),
+\item
+  the atmospheric surface pressure gradient effect on ocean and ice dynamics (\np[=.true.]{ln_apr_dyn}{ln\_apr\_dyn} with namelist \nam{sbc_apr}{sbc\_apr}),
+\item
+  the effect of sea-ice pressure on the ocean (\np[=.true.]{ln_ice_embd}{ln\_ice\_embd}).
 \end{itemize}
 
@@ -142 +144 @@
 The latter is the penetrative part of the heat flux.
 It is applied as a 3D trend of the temperature equation (\mdl{traqsr} module) when
-\np{ln_traqsr}{ln\_traqsr}\forcode{=.true.}.
+\np[=.true.]{ln_traqsr}{ln\_traqsr}.
 The way the light penetrates inside the water column is generally a sum of decreasing exponentials
 (see \autoref{subsec:TRA_qsr}).
@@ -278 +280 @@
                                   &  daily or weekLL     &  monthly           &  yearly        \\
       \hline
-      \np{clim}{clim}\forcode{=.false.} &  fn\_yYYYYmMMdDD.nc  &  fn\_yYYYYmMM.nc   &  fn\_yYYYY.nc  \\
+      \np[=.false.]{clim}{clim} &  fn\_yYYYYmMMdDD.nc  &  fn\_yYYYYmMM.nc   &  fn\_yYYYY.nc  \\
       \hline
-      \np{clim}{clim}\forcode{=.true.}  &  not possible        &  fn\_m??.nc        &  fn            \\
+      \np[=.true.]{clim}{clim}  &  not possible        &  fn\_m??.nc        &  fn            \\
       \hline
     \end{tabular}
@@ -351 +353 @@
 However, for forcing data related to the surface module,
 values are not needed at every time-step but at every \np{nn_fsbc}{nn\_fsbc} time-step.
-For example with \np{nn_fsbc}{nn\_fsbc}\forcode{=3}, the surface module will be called at time-steps 1, 4, 7, etc.
+For example with \np[=3]{nn_fsbc}{nn\_fsbc}, the surface module will be called at time-steps 1, 4, 7, etc.
 The date used for the time interpolation is thus redefined to the middle of \np{nn_fsbc}{nn\_fsbc} time-step period.
 In the previous example, this leads to: 1h30'00", 4h30'00", 7h30'00", etc. \\
@@ -550 +552 @@
   Spinup of the iceberg floats
 \item
-  Ocean/sea-ice simulation with both models running in parallel (\np{ln_mixcpl}{ln\_mixcpl}\forcode{=.true.})
+  Ocean/sea-ice simulation with both models running in parallel (\np[=.true.]{ln_mixcpl}{ln\_mixcpl})
 \end{itemize}
 
@@ -605 +607 @@
 
 The user can also choose in the \nam{sbc_sas}{sbc\_sas} namelist to read the mean (nn\_fsbc time-step) fraction of solar net radiation absorbed in the 1st T level using
- (\np{ln_flx}{ln\_flx}\forcode{=.true.}) and to provide 3D oceanic velocities instead of 2D ones (\np{ln_flx}{ln\_flx}\forcode{=.true.}). In that last case, only the 1st level will be read in.
+ (\np[=.true.]{ln_flx}{ln\_flx}) and to provide 3D oceanic velocities instead of 2D ones (\np{ln_flx}{ln\_flx}\forcode{=.true.}). In that last case, only the 1st level will be read in.
 
 
@@ -623 +625 @@
 %-------------------------------------------------------------------------------------------------------------
 
-In the flux formulation (\np{ln_flx}{ln\_flx}\forcode{=.true.}),
+In the flux formulation (\np[=.true.]{ln_flx}{ln\_flx}),
 the surface boundary condition fields are directly read from input files.
 The user has to define in the namelist \nam{sbc_flx}{sbc\_flx} the name of the file,
@@ -731 +733 @@
 \begin{itemize}
 \item
-  NCAR (\np{ln_NCAR}{ln\_NCAR}\forcode{=.true.}):
+  NCAR (\np[=.true.]{ln_NCAR}{ln\_NCAR}):
   The NCAR bulk formulae have been developed by \citet{large.yeager_rpt04}.
   They have been designed to handle the NCAR forcing, a mixture of NCEP reanalysis and satellite data.
@@ -741 +743 @@
   This is the so-called DRAKKAR Forcing Set (DFS) \citep{brodeau.barnier.ea_OM10}.
 \item
-  COARE 3.0 (\np{ln_COARE_3p0}{ln\_COARE\_3p0}\forcode{=.true.}):
+  COARE 3.0 (\np[=.true.]{ln_COARE_3p0}{ln\_COARE\_3p0}):
   See \citet{fairall.bradley.ea_JC03} for more details
 \item
-  COARE 3.5 (\np{ln_COARE_3p5}{ln\_COARE\_3p5}\forcode{=.true.}):
+  COARE 3.5 (\np[=.true.]{ln_COARE_3p5}{ln\_COARE\_3p5}):
   See \citet{edson.jampana.ea_JPO13} for more details
 \item
-  ECMWF (\np{ln_ECMWF}{ln\_ECMWF}\forcode{=.true.}):
+  ECMWF (\np[=.true.]{ln_ECMWF}{ln\_ECMWF}):
   Based on \href{https://www.ecmwf.int/node/9221}{IFS (Cy31)} implementation and documentation.
   Surface roughness lengths needed for the Obukhov length are computed following \citet{beljaars_QJRMS95}.
@@ -762 +764 @@
 \begin{itemize}
 \item
-  Constant value (\np{constant value}{constant\ value}\forcode{ Cd_ice = 1.4e-3 }):
+  Constant value (\np[ Cd_ice=1.4e-3 ]{constant value}{constant\ value}):
   default constant value used for momentum and heat neutral transfer coefficients
 \item
-  \citet{lupkes.gryanik.ea_JGR12} (\np{ln_Cd_L12}{ln\_Cd\_L12}\forcode{=.true.}):
+  \citet{lupkes.gryanik.ea_JGR12} (\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,
@@ -773 +775 @@
   It is theoretically applicable to all ice conditions (not only MIZ).
 \item
-  \citet{lupkes.gryanik_JGR15} (\np{ln_Cd_L15}{ln\_Cd\_L15}\forcode{=.true.}):
+  \citet{lupkes.gryanik_JGR15} (\np[=.true.]{ln_Cd_L15}{ln\_Cd\_L15}):
   Alternative turbulent transfer coefficients formulation between sea-ice
   and atmosphere with distinct momentum and heat coefficients depending
@@ -842 +844 @@
 
 The optional atmospheric pressure can be used to force ocean and ice dynamics
-(\np{ln_apr_dyn}{ln\_apr\_dyn}\forcode{=.true.}, \nam{sbc}{sbc} namelist).
+(\np[=.true.]{ln_apr_dyn}{ln\_apr\_dyn}, \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.
@@ -914 +916 @@
 computationally too expensive. Here, two options are available:
 $\Pi_{sal}$ generated by an external model can be read in
-(\np{ln_read_load}{ln\_read\_load}\forcode{ =.true.}), or a ``scalar approximation'' can be
-used (\np{ln_scal_load}{ln\_scal\_load}\forcode{ =.true.}). In the latter case
+(\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
 \[
   \Pi_{sal} = \beta \eta,
@@ -1076 +1078 @@
 \begin{description}
 
-  \item[\np{nn_isf}{nn\_isf}\forcode{=1}]:
-  The ice shelf cavity is represented (\np{ln_isfcav}{ln\_isfcav}\forcode{=.true.} needed).
+  \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.
 
@@ -1083 +1085 @@
 
    \begin{description}
-   \item[\np{nn_isfblk}{nn\_isfblk}\forcode{=1}]:
+   \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{nn_isfblk}{nn\_isfblk}\forcode{=2}]:
+   \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).
@@ -1103 +1105 @@
      There are 3 different ways to compute the exchange coeficient:
    \begin{description}
-        \item[\np{nn_gammablk}{nn\_gammablk}\forcode{=0}]:
+        \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*}
@@ -1111 +1113 @@
      \end{gather*}
      This is the recommended formulation for ISOMIP.
-   \item[\np{nn_gammablk}{nn\_gammablk}\forcode{=1}]:
+   \item[{\np[=1]{nn_gammablk}{nn\_gammablk}}]:
      The salt and heat exchange coefficients are velocity dependent and defined as
      \begin{gather*}
@@ -1119 +1121 @@
      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{nn_gammablk}{nn\_gammablk}\forcode{=2}]:
+   \item[{\np[=2]{nn_gammablk}{nn\_gammablk}}]:
      The salt and heat exchange coefficients are velocity and stability dependent and defined as:
 \[
@@ -1130 +1132 @@
      This formulation has not been extensively tested in \NEMO\ (not recommended).
    \end{description}
-  \item[\np{nn_isf}{nn\_isf}\forcode{=2}]:
+  \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{nn_isf}{nn\_isf}\forcode{=3}).
+   (\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{nn_isf}{nn\_isf}\forcode{=3}]:
+  \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
@@ -1143 +1145 @@
    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{nn_isf}{nn\_isf}\forcode{=4}]:
-   The ice shelf cavity is opened (\np{ln_isfcav}{ln\_isfcav}\forcode{=.true.} needed).
+  \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{nn_isf}{nn\_isf}\forcode{=1}, the fluxes are spread over the top boundary layer thickness (\np{rn_hisf_tbl}{rn\_hisf\_tbl})\\
+   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{nn_isf}{nn\_isf}\forcode{=1} and \np{nn_isf}{nn\_isf}\forcode{=2} compute a melt rate based on
+$\bullet$ \np[=1]{nn_isf}{nn\_isf} and \np[=2]{nn_isf}{nn\_isf} 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{nn_isf}{nn\_isf}\forcode{=3} and \np{nn_isf}{nn\_isf}\forcode{=4} read the melt rate from a file.
+$\bullet$ \np[=3]{nn_isf}{nn\_isf} and \np[=4]{nn_isf}{nn\_isf} 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
@@ -1204 +1206 @@
 \end{description}
 
-If \np{ln_iscpl}{ln\_iscpl}\forcode{=.true.}, the isf draft is assume to be different at each restart step with
+If \np[=.true.]{ln_iscpl}{ln\_iscpl}, 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:
@@ -1240 +1242 @@
 
 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{ln_hsb}{ln\_hsb}\forcode{=.true.}.
+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.
@@ -1270 +1272 @@
 which is an integer representing how many icebergs of this class are being described as one lagrangian point
 (this reduces the numerical problem of tracking every single iceberg).
-They are enabled by setting \np{ln_icebergs}{ln\_icebergs}\forcode{=.true.}.
+They are enabled by setting \np[=.true.]{ln_icebergs}{ln\_icebergs}.
 
 Two initialisation schemes are possible.
 \begin{description}
-\item[\np{nn_test_icebergs}{nn\_test\_icebergs}~$>$~0]
+\item[{\np{nn_test_icebergs}{nn\_test\_icebergs}~$>$~0}]
   In this scheme, the value of \np{nn_test_icebergs}{nn\_test\_icebergs} represents the class of iceberg to generate
   (so between 1 and 10), and \np{nn_test_icebergs}{nn\_test\_icebergs} provides a lon/lat box in the domain at each grid point of
@@ -1281 +1283 @@
   \np{nn_test_icebergs}{nn\_test\_icebergs} is defined by four numbers in \np{nn_test_box}{nn\_test\_box} representing the corners of
   the geographical box: lonmin,lonmax,latmin,latmax
-\item[\np{nn_test_icebergs}{nn\_test\_icebergs}\forcode{=-1}]
+\item[{\np[=-1]{nn_test_icebergs}{nn\_test\_icebergs}}]
   In this scheme, the model reads a calving file supplied in the \np{sn_icb}{sn\_icb} parameter.
   This should be a file with a field on the configuration grid (typically ORCA)
@@ -1306 +1308 @@
 The amount of information is controlled by two integer parameters:
 \begin{description}
-\item[\np{nn_verbose_level}{nn\_verbose\_level}] takes a value between one and four and
+\item[{\np{nn_verbose_level}{nn\_verbose\_level}}] takes a value between one and four and
   represents an increasing number of points in the code at which variables are written,
   and an increasing level of obscurity.
-\item[\np{nn_verbose_write}{nn\_verbose\_write}] is the number of timesteps between writes
+\item[{\np{nn_verbose_write}{nn\_verbose\_write}}] is the number of timesteps between writes
 \end{description}
 
@@ -1343 +1345 @@
 
 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}{sbc} namelist. In addition, specific flags accounting for
+\np[=.true.]{ln_wave}{ln\_wave} in \nam{sbc}{sbc} namelist. In addition, specific flags accounting for
 different processes should be activated as explained in the following sections.
 
@@ -1351 +1353 @@
 for external data names, locations, frequency, interpolation and all the miscellanous options allowed by
 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.}
+\item[coupled mode]: \NEMO\ and an external wave model can be coupled by setting \np[=.true.]{ln_cpl}{ln\_cpl}
 in \nam{sbc}{sbc} namelist and filling the \nam{sbc_cpl}{sbc\_cpl} namelist.
 \end{description}
@@ -1364 +1366 @@
 
 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}{sbc} namelist.
+can be used by setting the logical variable \np[=.true.]{ln_cdgw}{ln\_cdgw} 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
@@ -1408 +1410 @@
 
 \begin{description}
-\item[\np{nn_sdrift}{nn\_sdrift} = 0]: exponential integral profile parameterization proposed by
+\item[{\np{nn_sdrift}{nn\_sdrift} = 0}]: exponential integral profile parameterization proposed by
 \citet{breivik.janssen.ea_JPO14}:
 
@@ -1427 +1429 @@
 where $H_s$ is the significant wave height and $\omega$ is the wave frequency.
 
-\item[\np{nn_sdrift}{nn\_sdrift} = 1]: velocity profile based on the Phillips spectrum which is considered to be a
+\item[{\np{nn_sdrift}{nn\_sdrift} = 1}]: velocity profile based on the Phillips spectrum which is considered to be a
 reasonable estimate of the part of the spectrum mostly contributing to the Stokes drift velocity near the surface
 \citep{breivik.bidlot.ea_OM16}:
@@ -1439 +1441 @@
 where $erf$ is the complementary error function and $k_p$ is the peak wavenumber.
 
-\item[\np{nn_sdrift}{nn\_sdrift} = 2]: velocity profile based on the Phillips spectrum as for \np{nn_sdrift}{nn\_sdrift} = 1
+\item[{\np{nn_sdrift}{nn\_sdrift} = 2}]: velocity profile based on the Phillips spectrum as for \np{nn_sdrift}{nn\_sdrift} = 1
 but using the wave frequency from a wave model.
 
@@ -1477 +1479 @@
 In order to include this term, once evaluated the Stokes drift (using one of the 3 possible
 approximations described in \autoref{subsec:SBC_wave_sdw}),
-\np{ln_stcor}{ln\_stcor}\forcode{=.true.} has to be set.
+\np[=.true.]{ln_stcor}{ln\_stcor} has to be set.
 
 
@@ -1517 +1519 @@
 
 The wave stress derived from an external wave model can be provided either through the normalized
-wave stress into the ocean by setting \np{ln_tauwoc}{ln\_tauwoc}\forcode{=.true.}, or through the zonal and
-meridional stress components by setting \np{ln_tauw}{ln\_tauw}\forcode{=.true.}.
+wave stress into the ocean by setting \np[=.true.]{ln_tauwoc}{ln\_tauwoc}, or through the zonal and
+meridional stress components by setting \np[=.true.]{ln_tauw}{ln\_tauw}.
 
 
@@ -1561 +1563 @@
 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}{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.}).
+setting \np[=.true.]{ln_dm2dc}{ln\_dm2dc} (a \textit{\nam{sbc}{sbc}} namelist variable) when
+using a bulk formulation (\np[=.true.]{ln_blk}{ln\_blk}) or
+the flux formulation (\np[=.true.]{ln_flx}{ln\_flx}).
 The reconstruction is performed in the \mdl{sbcdcy} module.
 The detail of the algoritm used can be found in the appendix~A of \cite{bernie.guilyardi.ea_CD07}.
@@ -1598 +1600 @@
 \label{subsec:SBC_rotation}
 
-When using a flux (\np{ln_flx}{ln\_flx}\forcode{=.true.}) or bulk (\np{ln_blk}{ln\_blk}\forcode{=.true.}) formulation,
+When using a flux (\np[=.true.]{ln_flx}{ln\_flx}) or bulk (\np[=.true.]{ln_blk}{ln\_blk}) formulation,
 pairs of vector components can be rotated from east-north directions onto the local grid directions.
 This is particularly useful when interpolation on the fly is used since here any vectors are likely to
@@ -1627 +1629 @@
 
 Options are defined through the \nam{sbc_ssr}{sbc\_ssr} namelist variables.
-On forced mode using a flux formulation (\np{ln_flx}{ln\_flx}\forcode{=.true.}),
+On forced mode using a flux formulation (\np[=.true.]{ln_flx}{ln\_flx}),
 a feedback term \emph{must} be added to the surface heat flux $Q_{ns}^o$:
 \[
@@ -1746 +1748 @@
 
 \begin{description}
-\item[\np{nn_fwb}{nn\_fwb}\forcode{=0}]
+\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{nn_fwb}{nn\_fwb}\forcode{=1}]
+\item[{\np[=1]{nn_fwb}{nn\_fwb}}]
   global mean \textit{emp} 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{nn_fwb}{nn\_fwb}\forcode{=2}]
+\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.
@@ -1783 +1785 @@
 
 
-\biblio
-
-\pindex
+\onlyinsubfile{\bibliography{../main/bibliography}}
+
+\onlyinsubfile{\printindex}
 
 \end{document}