Changeset 11582


Ignore:
Timestamp:
2019-09-20T11:44:31+02:00 (12 months 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[]{}{}

Location:
NEMO/trunk/doc/latex/NEMO/subfiles
Files:
24 edited

Legend:

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

    r11578 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    5557 
    5658\begin{description} 
    57  \item[\np{jphgr_mesh}{jphgr\_mesh}=0]  The most general curvilinear orthogonal grids. 
     59 \item[{\np{jphgr_mesh}{jphgr\_mesh}=0}]  The most general curvilinear orthogonal grids. 
    5860  The coordinates and their first derivatives with respect to $i$ and $j$ are provided 
    5961  in a input file (\ifile{coordinates}), read in \rou{hgr\_read} subroutine of the domhgr module. 
    6062  This is now the only option available within \NEMO\ itself from v4.0 onwards. 
    61 \item[\np{jphgr_mesh}{jphgr\_mesh}=1 to 5] A few simple analytical grids are provided (see below). 
     63\item[{\np{jphgr_mesh}{jphgr\_mesh}=1 to 5}] A few simple analytical grids are provided (see below). 
    6264  For other analytical grids, the \mdl{domhgr} module (\texttt{DOMAINcfg} variant) must be 
    6365  modified by the user. In most cases, modifying the \mdl{usrdef\_hgr} module of \NEMO\ is 
     
    136138 
    137139It is possible to define a simple regular vertical grid by giving zero stretching 
    138 (\np{ppacr}{ppacr}\forcode{ = 0}).  In that case, the parameters \jp{jpk} (number of $w$-levels) 
     140(\np[=0]{ppacr}{ppacr}).  In that case, the parameters \jp{jpk} (number of $w$-levels) 
    139141and \np{pphmax}{pphmax} (total ocean depth in meters) fully define the grid. 
    140142 
     
    152154top and bottom with a smooth hyperbolic tangent transition in between (\autoref{fig:DOMCFG_zgr}). 
    153155 
    154 A double hyperbolic tangent version (\np{ldbletanh}{ldbletanh}\forcode{ = .true.}) is also available 
     156A double hyperbolic tangent version (\np[=.true.]{ldbletanh}{ldbletanh}) is also available 
    155157which permits finer control and is used, typically, to obtain a well resolved upper ocean 
    156158without compromising on resolution at depth using a moderate number of levels. 
     
    170172\end{gather} 
    171173 
    172 If the ice shelf cavities are opened (\np{ln_isfcav}{ln\_isfcav}\forcode{ = .true.}), the definition 
     174If the ice shelf cavities are opened (\np[=.true.]{ln_isfcav}{ln\_isfcav}), the definition 
    173175of $z_0$ is the same.  However, definition of $e_3^0$ at $t$- and $w$-points is 
    174176respectively changed to: 
     
    314316\np{nn_bathy}{nn\_bathy} (found in \nam{dom}{dom} namelist (\texttt{DOMAINCFG} variant) ): 
    315317\begin{description} 
    316 \item[\np{nn_bathy}{nn\_bathy}\forcode{ = 0}]: 
     318\item[{\np[=0]{nn_bathy}{nn\_bathy}}]: 
    317319  a flat-bottom domain is defined. 
    318320  The total depth $z_w (jpk)$ is given by the coordinate transformation. 
    319321  The domain can either be a closed basin or a periodic channel depending on the parameter \np{jperio}{jperio}. 
    320 \item[\np{nn_bathy}{nn\_bathy}\forcode{ = -1}]: 
     322\item[{\np[=-1]{nn_bathy}{nn\_bathy}}]: 
    321323  a domain with a bump of topography one third of the domain width at the central latitude. 
    322324  This is meant for the "EEL-R5" configuration, a periodic or open boundary channel with a seamount. 
    323 \item[\np{nn_bathy}{nn\_bathy}\forcode{ = 1}]: 
     325\item[{\np[=1]{nn_bathy}{nn\_bathy}}]: 
    324326  read a bathymetry and ice shelf draft (if needed). 
    325327  The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters) at 
     
    332334  The \ifile{isfdraft\_meter} file (Netcdf format) provides the ice shelf draft (positive, in meters) at 
    333335  each grid point of the model grid. 
    334   This file is only needed if \np{ln_isfcav}{ln\_isfcav}\forcode{ = .true.}. 
     336  This file is only needed if \np[=.true.]{ln_isfcav}{ln\_isfcav}. 
    335337  Defining the ice shelf draft will also define the ice shelf edge and the grounding line position. 
    336338\end{description} 
     
    412414%-------------------------------------------------------------------------------------------------------------- 
    413415Options are defined in \nam{zgr_sco}{zgr\_sco} (\texttt{DOMAINcfg} only). 
    414 In $s$-coordinate (\np{ln_sco}{ln\_sco}\forcode{ = .true.}), the depth and thickness of the model levels are defined from 
     416In $s$-coordinate (\np[=.true.]{ln_sco}{ln\_sco}), the depth and thickness of the model levels are defined from 
    415417the product of a depth field and either a stretching function or its derivative, respectively: 
    416418 
     
    435437 
    436438The original default \NEMO\ s-coordinate stretching is available if neither of the other options are specified as true 
    437 (\np{ln_s_SH94}{ln\_s\_SH94}\forcode{ = .false.} and \np{ln_s_SF12}{ln\_s\_SF12}\forcode{ = .false.}). 
     439(\np[=.false.]{ln_s_SH94}{ln\_s\_SH94} and \np[=.false.]{ln_s_SF12}{ln\_s\_SF12}). 
    438440This uses a depth independent $\tanh$ function for the stretching \citep{madec.delecluse.ea_JPO96}: 
    439441 
     
    455457 
    456458A stretching function, 
    457 modified from the commonly used \citet{song.haidvogel_JCP94} stretching (\np{ln_s_SH94}{ln\_s\_SH94}\forcode{ = .true.}), 
     459modified from the commonly used \citet{song.haidvogel_JCP94} stretching (\np[=.true.]{ln_s_SH94}{ln\_s\_SH94}), 
    458460is also available and is more commonly used for shelf seas modelling: 
    459461 
     
    558560This option is described in the Report by Levier \textit{et al.} (2007), available on the \NEMO\ web site. 
    559561 
    560 \biblio 
    561  
    562 \pindex 
     562\onlyinsubfile{\bibliography{../main/bibliography}} 
     563 
     564\onlyinsubfile{\printindex} 
    563565 
    564566\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_algos.tex

    r11577 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    1719%        UBS scheme 
    1820% ------------------------------------------------------------------------------------------------------------- 
    19 \section{Upstream Biased Scheme (UBS) (\protect\np{ln_traadv_ubs}{ln\_traadv\_ubs}\forcode{ = .true.})} 
     21\section{Upstream Biased Scheme (UBS) (\protect\np[=.true.]{ln_traadv_ubs}{ln\_traadv\_ubs})} 
    2022\label{sec:ALGOS_tra_adv_ubs} 
    2123 
     
    5961the control of artificial diapycnal fluxes is of paramount importance. 
    6062It has therefore been preferred to evaluate the vertical flux using the TVD scheme when 
    61 \np{ln_traadv_ubs}{ln\_traadv\_ubs}\forcode{ = .true.}. 
     63\np[=.true.]{ln_traadv_ubs}{ln\_traadv\_ubs}. 
    6264 
    6365For stability reasons, in \autoref{eq:TRA_adv_ubs}, the first term which corresponds to 
     
    841843\ie\ the variance of the tracer is preserved by the discretisation of the skew fluxes. 
    842844 
    843 \biblio 
    844  
    845 \pindex 
     845\onlyinsubfile{\bibliography{../main/bibliography}} 
     846 
     847\onlyinsubfile{\printindex} 
    846848 
    847849\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_diff_opers.tex

    r11558 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    411413that is a Laplacian diffusion is applied on momentum along the coordinate directions. 
    412414 
    413 \biblio 
    414  
    415 \pindex 
     415\onlyinsubfile{\bibliography{../main/bibliography}} 
     416 
     417\onlyinsubfile{\printindex} 
    416418 
    417419\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_invariants.tex

    r11577 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    366368%       Vorticity Term with ENE scheme 
    367369% ------------------------------------------------------------------------------------------------------------- 
    368 \subsubsection{Vorticity term with ENE scheme (\protect\np{ln_dynvor_ene}{ln\_dynvor\_ene}\forcode{ = .true.})} 
     370\subsubsection{Vorticity term with ENE scheme (\protect\np[=.true.]{ln_dynvor_ene}{ln\_dynvor\_ene})} 
    369371\label{subsec:INVARIANTS_vorENE} 
    370372 
     
    406408%       Vorticity Term with EEN scheme 
    407409% ------------------------------------------------------------------------------------------------------------- 
    408 \subsubsection{Vorticity term with EEN scheme (\protect\np{ln_dynvor_een}{ln\_dynvor\_een}\forcode{ = .true.})} 
     410\subsubsection{Vorticity term with EEN scheme (\protect\np[=.true.]{ln_dynvor_een}{ln\_dynvor\_een})} 
    409411\label{subsec:INVARIANTS_vorEEN_vect} 
    410412 
     
    878880%       Vorticity Term with ENS scheme 
    879881% ------------------------------------------------------------------------------------------------------------- 
    880 \subsubsection{Vorticity term with ENS scheme  (\protect\np{ln_dynvor_ens}{ln\_dynvor\_ens}\forcode{ = .true.})} 
     882\subsubsection{Vorticity term with ENS scheme  (\protect\np[=.true.]{ln_dynvor_ens}{ln\_dynvor\_ens})} 
    881883\label{subsec:INVARIANTS_vorENS} 
    882884 
     
    947949%       Vorticity Term with EEN scheme 
    948950% ------------------------------------------------------------------------------------------------------------- 
    949 \subsubsection{Vorticity Term with EEN scheme (\protect\np{ln_dynvor_een}{ln\_dynvor\_een}\forcode{ = .true.})} 
     951\subsubsection{Vorticity Term with EEN scheme (\protect\np[=.true.]{ln_dynvor_een}{ln\_dynvor\_een})} 
    950952\label{subsec:INVARIANTS_vorEEN} 
    951953 
     
    15281530%%%%  end of appendix in gm comment 
    15291531%} 
    1530 \biblio 
    1531  
    1532 \pindex 
     1532\onlyinsubfile{\bibliography{../main/bibliography}} 
     1533 
     1534\onlyinsubfile{\printindex} 
    15331535 
    15341536\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_s_coord.tex

    r11558 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    594596the expression of the 3D divergence in the $s-$coordinates established above. 
    595597 
    596 \biblio 
    597  
    598 \pindex 
     598\onlyinsubfile{\bibliography{../main/bibliography}} 
     599 
     600\onlyinsubfile{\printindex} 
    599601 
    600602\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_triads.tex

    r11577 r11582  
    1111\newcommand{\rtriadt}[1]{\ensuremath{\triadt{i}{k}{#1}{i_p}{k_p}}} 
    1212 
     13\onlyinsubfile{\makeindex} 
     14 
    1315\begin{document} 
    1416% ================================================================ 
     
    4244The options specific to the Griffies scheme include: 
    4345\begin{description} 
    44 \item[\np{ln_triad_iso}{ln\_triad\_iso}] 
     46\item[{\np{ln_triad_iso}{ln\_triad\_iso}}] 
    4547  See \autoref{sec:TRIADS_taper}. 
    4648  If this is set false (the default), 
     
    5355  giving an almost pure horizontal diffusive tracer flux within the mixed layer. 
    5456  This is similar to the tapering suggested by \citet{gerdes.koberle.ea_CD91}. See \autoref{subsec:TRIADS_Gerdes-taper} 
    55 \item[\np{ln_botmix_triad}{ln\_botmix\_triad}] 
     57\item[{\np{ln_botmix_triad}{ln\_botmix\_triad}}] 
    5658  See \autoref{sec:TRIADS_iso_bdry}. 
    5759  If this is set false (the default) then the lateral diffusive fluxes 
     
    5961  If it is set true, however, then these lateral diffusive fluxes are applied, 
    6062  giving smoother bottom tracer fields at the cost of introducing diapycnal mixing. 
    61 \item[\np{rn_sw_triad}{rn\_sw\_triad}] 
     63\item[{\np{rn_sw_triad}{rn\_sw\_triad}}] 
    6264  blah blah to be added.... 
    6365\end{description} 
    6466The options shared with the Standard scheme include: 
    6567\begin{description} 
    66 \item[\np{ln_traldf_msc}{ln\_traldf\_msc}]   blah blah to be added 
    67 \item[\np{rn_slpmax}{rn\_slpmax}]  blah blah to be added 
     68\item[{\np{ln_traldf_msc}{ln\_traldf\_msc}}]   blah blah to be added 
     69\item[{\np{rn_slpmax}{rn\_slpmax}}]  blah blah to be added 
    6870\end{description} 
    6971 
     
    646648Note that both near bottom triad slopes \triad{i}{k}{R}{1/2}{1/2} and \triad{i+1}{k}{R}{-1/2}{1/2} are masked when 
    647649either of the $i,k+1$ or $i+1,k+1$ tracer points is masked, \ie\ the $i,k+1$ $u$-point is masked. 
    648 The associated lateral fluxes (grey-black dashed line) are masked if \np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .false.}, 
    649 but left unmasked, giving bottom mixing, if \np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .true.}. 
    650  
    651 The default option \np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .false.} is suitable when the bbl mixing option is enabled 
    652 (\np{ln_trabbl}{ln\_trabbl}\forcode{ = .true.}, with \np{nn_bbl_ldf}{nn\_bbl\_ldf}\forcode{ = 1}), or for simple idealized problems. 
    653 For setups with topography without bbl mixing, \np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .true.} may be necessary. 
     650The associated lateral fluxes (grey-black dashed line) are masked if \np[=.false.]{ln_botmix_triad}{ln\_botmix\_triad}, 
     651but left unmasked, giving bottom mixing, if \np[=.true.]{ln_botmix_triad}{ln\_botmix\_triad}. 
     652 
     653The default option \np[=.false.]{ln_botmix_triad}{ln\_botmix\_triad} is suitable when the bbl mixing option is enabled 
     654(\np[=.true.]{ln_trabbl}{ln\_trabbl}, with \np[=1]{nn_bbl_ldf}{nn\_bbl\_ldf}), or for simple idealized problems. 
     655For setups with topography without bbl mixing, \np[=.true.]{ln_botmix_triad}{ln\_botmix\_triad} may be necessary. 
    654656% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    655657\begin{figure}[h] 
     
    672674    \ie\ the $i,k+1$ $u$-point is masked. 
    673675    The associated lateral fluxes (grey-black dashed line) are masked if 
    674     \protect\np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .false.}, but left unmasked, 
    675     giving bottom mixing, if \protect\np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .true.}} 
     676    \protect\np[=.false.]{ln_botmix_triad}{ln\_botmix\_triad}, but left unmasked, 
     677    giving bottom mixing, if \protect\np[=.true.]{ln_botmix_triad}{ln\_botmix\_triad}} 
    676678  \label{fig:TRIADS_bdry_triads} 
    677679\end{figure} 
     
    715717\label{sec:TRIADS_lintaper} 
    716718 
    717 This is the option activated by the default choice \np{ln_triad_iso}{ln\_triad\_iso}\forcode{ = .false.}. 
     719This is the option activated by the default choice \np[=.false.]{ln_triad_iso}{ln\_triad\_iso}. 
    718720Slopes $\tilde{r}_i$ relative to geopotentials are tapered linearly from their value immediately below 
    719721the mixed layer to zero at the surface, as described in option (c) of \autoref{fig:LDF_eiv_slp}, to values 
     
    11451147\label{sec:TRIADS_sfdiag} 
    11461148 
    1147 Where the namelist parameter \np{ln_traldf_gdia}{ln\_traldf\_gdia}\forcode{ = .true.}, 
     1149Where the namelist parameter \np[=.true.]{ln_traldf_gdia}{ln\_traldf\_gdia}, 
    11481150diagnosed mean eddy-induced velocities are output. 
    11491151Each time step, streamfunctions are calculated in the $i$-$k$ and $j$-$k$ planes at 
     
    11711173\] 
    11721174 
    1173 \biblio 
    1174  
    1175 \pindex 
     1175\onlyinsubfile{\bibliography{../main/bibliography}} 
     1176 
     1177\onlyinsubfile{\printindex} 
    11761178 
    11771179\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_ASM.tex

    r11578 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    194196\end{clines} 
    195197 
    196 \biblio 
    197  
    198 \pindex 
     198\onlyinsubfile{\bibliography{../main/bibliography}} 
     199 
     200\onlyinsubfile{\printindex} 
    199201 
    200202\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex

    r11578 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    125127 
    126128XIOS may be used to read single file restart produced by \NEMO. Currently only the variables written to 
    127 file \forcode{numror} can be handled by XIOS. To activate restart reading using XIOS, set \np{ln_xios_read}{ln\_xios\_read}\forcode{=.true. } 
     129file \forcode{numror} can be handled by XIOS. To activate restart reading using XIOS, set \np[=.true. ]{ln_xios_read}{ln\_xios\_read} 
    128130in \textit{namelist\_cfg}. This setting will be ignored when multiple restart files are present, and default \NEMO 
    129131functionality will be used for reading. There is no need to change iodef.xml file to use XIOS to read 
     
    143145type of restart \NEMO\ will write. If it is set to 0, default \NEMO\ functionality will be used - each 
    144146processor writes its own restart file; if it is set to 1 XIOS will write restart into a single file; 
    145 for \np{nn_wxios}{nn\_wxios}\forcode{=2} the restart will be written by XIOS into multiple files, one for each XIOS server. 
    146 Note, however, that \textbf{\NEMO\ will not read restart generated by XIOS when \np{nn_wxios}{nn\_wxios}\forcode{=2}}. The restart will 
     147for \np[=2]{nn_wxios}{nn\_wxios} the restart will be written by XIOS into multiple files, one for each XIOS server. 
     148Note, however, that \textbf{\NEMO\ will not read restart generated by XIOS when \np[=2]{nn_wxios}{nn\_wxios}}. The restart will 
    147149have to be rebuild before continuing the run. This option aims to reduce number of restart files generated by \NEMO\ only, 
    148150and may be useful when there is a need to change number of processors used to run simulation. 
     
    14701472 
    14711473\begin{description} 
    1472 \item[\np{ln_glo_trd}{ln\_glo\_trd}]: 
     1474\item[{\np{ln_glo_trd}{ln\_glo\_trd}}]: 
    14731475  at each \np{nn_trd}{nn\_trd} time-step a check of the basin averaged properties of 
    14741476  the momentum and tracer equations is performed. 
    14751477  This also includes a check of $T^2$, $S^2$, $\tfrac{1}{2} (u^2+v2)$, 
    14761478  and potential energy time evolution equations properties; 
    1477 \item[\np{ln_dyn_trd}{ln\_dyn\_trd}]: 
     1479\item[{\np{ln_dyn_trd}{ln\_dyn\_trd}}]: 
    14781480  each 3D trend of the evolution of the two momentum components is output; 
    1479 \item[\np{ln_dyn_mxl}{ln\_dyn\_mxl}]: 
     1481\item[{\np{ln_dyn_mxl}{ln\_dyn\_mxl}}]: 
    14801482  each 3D trend of the evolution of the two momentum components averaged over the mixed layer is output; 
    1481 \item[\np{ln_vor_trd}{ln\_vor\_trd}]: 
     1483\item[{\np{ln_vor_trd}{ln\_vor\_trd}}]: 
    14821484  a vertical summation of the moment tendencies is performed, 
    14831485  then the curl is computed to obtain the barotropic vorticity tendencies which are output; 
    1484 \item[\np{ln_KE_trd}{ln\_KE\_trd}] : 
     1486\item[{\np{ln_KE_trd}{ln\_KE\_trd}}] : 
    14851487  each 3D trend of the Kinetic Energy equation is output; 
    1486 \item[\np{ln_tra_trd}{ln\_tra\_trd}]: 
     1488\item[{\np{ln_tra_trd}{ln\_tra\_trd}}]: 
    14871489  each 3D trend of the evolution of temperature and salinity is output; 
    1488 \item[\np{ln_tra_mxl}{ln\_tra\_mxl}]: 
     1490\item[{\np{ln_tra_mxl}{ln\_tra\_mxl}}]: 
    14891491  each 2D trend of the evolution of temperature and salinity averaged over the mixed layer is output; 
    14901492\end{description} 
     
    14951497\textbf{Note that} in the current version (v3.6), many changes has been introduced but not fully tested. 
    14961498In particular, options associated with \np{ln_dyn_mxl}{ln\_dyn\_mxl}, \np{ln_vor_trd}{ln\_vor\_trd}, and \np{ln_tra_mxl}{ln\_tra\_mxl} are not working, 
    1497 and none of the options have been tested with variable volume (\ie\ \np{ln_linssh}{ln\_linssh}\forcode{=.true.}). 
     1499and none of the options have been tested with variable volume (\ie\ \np[=.true.]{ln_linssh}{ln\_linssh}). 
    14981500 
    14991501% ------------------------------------------------------------------------------------------------------------- 
     
    15151517Options are defined by \nam{flo}{flo} namelist variables. 
    15161518The algorithm used is based either on the work of \cite{blanke.raynaud_JPO97} (default option), 
    1517 or on a $4^th$ Runge-Hutta algorithm (\np{ln_flork4}{ln\_flork4}\forcode{=.true.}). 
     1519or on a $4^th$ Runge-Hutta algorithm (\np[=.true.]{ln_flork4}{ln\_flork4}). 
    15181520Note that the \cite{blanke.raynaud_JPO97} algorithm have the advantage of providing trajectories which 
    15191521are consistent with the numeric of the code, so that the trajectories never intercept the bathymetry. 
     
    15221524 
    15231525Initial coordinates can be given with Ariane Tools convention 
    1524 (IJK coordinates, (\np{ln_ariane}{ln\_ariane}\forcode{=.true.}) ) or with longitude and latitude. 
     1526(IJK coordinates, (\np[=.true.]{ln_ariane}{ln\_ariane}) ) or with longitude and latitude. 
    15251527 
    15261528In case of Ariane convention, input filename is \textit{init\_float\_ariane}. 
     
    15731575 
    15741576\np{jpnfl}{jpnfl} is the total number of floats during the run. 
    1575 When initial positions are read in a restart file (\np{ln_rstflo}{ln\_rstflo}\forcode{=.true.} ), 
     1577When initial positions are read in a restart file (\np[=.true.]{ln_rstflo}{ln\_rstflo} ), 
    15761578\np{jpnflnewflo}{jpnflnewflo} can be added in the initialization file. 
    15771579 
     
    15811583creation of the float restart file. 
    15821584 
    1583 Output data can be written in ascii files (\np{ln_flo_ascii}{ln\_flo\_ascii}\forcode{=.true.}). 
     1585Output data can be written in ascii files (\np[=.true.]{ln_flo_ascii}{ln\_flo\_ascii}). 
    15841586In that case, output filename is trajec\_float. 
    15851587 
    1586 Another possiblity of writing format is Netcdf (\np{ln_flo_ascii}{ln\_flo\_ascii}\forcode{=.false.}) with 
     1588Another possiblity of writing format is Netcdf (\np[=.false.]{ln_flo_ascii}{ln\_flo\_ascii}) with 
    15871589\key{iomput} and outputs selected in iodef.xml. 
    15881590Here it is an example of specification to put in files description section: 
     
    19391941 
    19401942Third, the discretisation of \autoref{eq:DIA_steric_Bq} depends on the type of free surface which is considered. 
    1941 In the non linear free surface case, \ie\ \np{ln_linssh}{ln\_linssh}\forcode{=.true.}, it is given by 
     1943In the non linear free surface case, \ie\ \np[=.true.]{ln_linssh}{ln\_linssh}, it is given by 
    19421944 
    19431945\[ 
     
    20342036sea water pressure at sea floor (botpres), dynamic sea surface height (sshdyn). 
    20352037 
    2036 In \mdl{diaptr} when \np{ln_diaptr}{ln\_diaptr}\forcode{=.true.} 
     2038In \mdl{diaptr} when \np[=.true.]{ln_diaptr}{ln\_diaptr} 
    20372039(see the \nam{ptr}{ptr} namelist below) can be computed on-line the poleward heat and salt transports, 
    20382040their advective and diffusive component, and the meriodional stream function . 
    2039 When \np{ln_subbas}{ln\_subbas}\forcode{=.true.}, transports and stream function are computed for the Atlantic, Indian, 
     2041When \np[=.true.]{ln_subbas}{ln\_subbas}, transports and stream function are computed for the Atlantic, Indian, 
    20402042Pacific and Indo-Pacific Oceans (defined north of 30\deg{S}) as well as for the World Ocean. 
    20412043The sub-basin decomposition requires an input file (\ifile{subbasins}) which contains three 2D mask arrays, 
     
    21192121% ================================================================ 
    21202122 
    2121 \biblio 
    2122  
    2123 \pindex 
     2123\onlyinsubfile{\bibliography{../main/bibliography}} 
     2124 
     2125\onlyinsubfile{\printindex} 
    21242126 
    21252127\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIU.tex

    r11578 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    4648This namelist contains only two variables: 
    4749\begin{description} 
    48 \item[\np{ln_diurnal}{ln\_diurnal}] 
     50\item[{\np{ln_diurnal}{ln\_diurnal}}] 
    4951  A logical switch for turning on/off both the cool skin and warm layer. 
    50 \item[\np{ln_diurnal_only}{ln\_diurnal\_only}] 
     52\item[{\np{ln_diurnal_only}{ln\_diurnal\_only}}] 
    5153  A logical switch which if \forcode{.true.} will run the diurnal model without the other dynamical parts of \NEMO. 
    5254  \np{ln_diurnal_only}{ln\_diurnal\_only} must be \forcode{.false.} if \np{ln_diurnal}{ln\_diurnal} is \forcode{.false.}. 
     
    159161\] 
    160162 
    161 \biblio 
     163\onlyinsubfile{\bibliography{../main/bibliography}} 
    162164 
    163 \pindex 
     165\onlyinsubfile{\printindex} 
    164166 
    165167\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex

    r11578 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    487489    (d) hybrid $s-z$ coordinate, 
    488490    (e) hybrid $s-z$ coordinate with partial step, and 
    489     (f) same as (e) but in the non-linear free surface (\protect\np{ln_linssh}{ln\_linssh}\forcode{=.false.}). 
     491    (f) same as (e) but in the non-linear free surface (\protect\np[=.false.]{ln_linssh}{ln\_linssh}). 
    490492    Note that the non-linear free surface can be used with any of the 5 coordinates (a) to (e).} 
    491493  \label{fig:DOM_z_zps_s_sps} 
     
    524526 
    525527\begin{itemize} 
    526 \item $z$-coordinate with full step bathymetry (\np{ln_zco}{ln\_zco}\forcode{=.true.}), 
    527 \item $z$-coordinate with partial step ($zps$) bathymetry (\np{ln_zps}{ln\_zps}\forcode{=.true.}), 
    528 \item Generalized, $s$-coordinate (\np{ln_sco}{ln\_sco}\forcode{=.true.}). 
     528\item $z$-coordinate with full step bathymetry (\np[=.true.]{ln_zco}{ln\_zco}), 
     529\item $z$-coordinate with partial step ($zps$) bathymetry (\np[=.true.]{ln_zps}{ln\_zps}), 
     530\item Generalized, $s$-coordinate (\np[=.true.]{ln_sco}{ln\_sco}). 
    529531\end{itemize} 
    530532 
     
    544546They are updated at each model time step. 
    545547The initial fixed reference coordinate system is held in variable names with a $\_0$ suffix. 
    546 When the linear free surface option is used (\np{ln_linssh}{ln\_linssh}\forcode{=.true.}), 
     548When the linear free surface option is used (\np[=.true.]{ln_linssh}{ln\_linssh}), 
    547549\textit{before}, \textit{now} and \textit{after} arrays are initially set to 
    548550their reference counterpart and remain fixed. 
     
    682684 
    683685\begin{description} 
    684 \item[\np{ln_tsd_init}{ln\_tsd\_init}\forcode{= .true.}] 
     686\item[{\np[=.true.]{ln_tsd_init}{ln\_tsd\_init}}] 
    685687  Use T and S input files that can be given on the model grid itself or on their native input data grids. 
    686688  In the latter case, the data will be interpolated on-the-fly both in the horizontal and the vertical to the model grid 
     
    688690  The information relating to the input files are specified in the \np{sn_tem}{sn\_tem} and \np{sn_sal}{sn\_sal} structures. 
    689691  The computation is done in the \mdl{dtatsd} module. 
    690 \item[\np{ln_tsd_init}{ln\_tsd\_init}\forcode{= .false.}] 
     692\item[{\np[=.false.]{ln_tsd_init}{ln\_tsd\_init}}] 
    691693  Initial values for T and S are set via a user supplied \rou{usr\_def\_istate} routine contained in \mdl{userdef\_istate}. 
    692694  The default version sets horizontally uniform T and profiles as used in the GYRE configuration 
     
    694696\end{description} 
    695697 
    696 \biblio 
    697  
    698 \pindex 
     698\onlyinsubfile{\bibliography{../main/bibliography}} 
     699 
     700\onlyinsubfile{\printindex} 
    699701 
    700702\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex

    r11578 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    205207(EEN scheme) (see \autoref{subsec:INVARIANTS_vorEEN}). 
    206208In the case of ENS, ENE or MIX schemes the land sea mask may be slightly modified to ensure the consistency of 
    207 vorticity term with analytical equations (\np{ln_dynvor_con}{ln\_dynvor\_con}\forcode{=.true.}). 
     209vorticity term with analytical equations (\np[=.true.]{ln_dynvor_con}{ln\_dynvor\_con}). 
    208210The vorticity terms are all computed in dedicated routines that can be found in the \mdl{dynvor} module. 
    209211 
     
    327329A key point in \autoref{eq:DYN_een_e3f} is how the averaging in the \textbf{i}- and \textbf{j}- directions is made. 
    328330It uses the sum of masked t-point vertical scale factor divided either by the sum of the four t-point masks 
    329 (\np{nn_een_e3f}{nn\_een\_e3f}\forcode{=1}), or just by $4$ (\np{nn_een_e3f}{nn\_een\_e3f}\forcode{=.true.}). 
     331(\np[=1]{nn_een_e3f}{nn\_een\_e3f}), or just by $4$ (\np[=.true.]{nn_een_e3f}{nn\_een\_e3f}). 
    330332The latter case preserves the continuity of $e_{3f}$ when one or more of the neighbouring $e_{3t}$ tends to zero and 
    331333extends by continuity the value of $e_{3f}$ into the land areas. 
     
    407409  \right. 
    408410\] 
    409 When \np{ln_dynzad_zts}{ln\_dynzad\_zts}\forcode{=.true.}, 
     411When \np[=.true.]{ln_dynzad_zts}{ln\_dynzad\_zts}, 
    410412a split-explicit time stepping with 5 sub-timesteps is used on the vertical advection term. 
    411413This option can be useful when the value of the timestep is limited by vertical advection \citep{lemarie.debreu.ea_OM15}. 
     
    534536But the amplitudes of the false extrema are significantly reduced over those in the centred second order method. 
    535537As the scheme already includes a diffusion component, it can be used without explicit lateral diffusion on momentum 
    536 (\ie\ \np{ln_dynldf_lap}{ln\_dynldf\_lap}\forcode{=}\np{ln_dynldf_bilap}{ln\_dynldf\_bilap}\forcode{=.false.}), 
     538(\ie\ \np[=]{ln_dynldf_lap}{ln\_dynldf\_lap}\np[=.false.]{ln_dynldf_bilap}{ln\_dynldf\_bilap}), 
    537539and it is recommended to do so. 
    538540 
     
    665667density Jacobian with cubic polynomial method is currently disabled whilst known bugs are under investigation. 
    666668 
    667 $\bullet$ Traditional coding (see for example \citet{madec.delecluse.ea_JPO96}: (\np{ln_dynhpg_sco}{ln\_dynhpg\_sco}\forcode{=.true.}) 
     669$\bullet$ Traditional coding (see for example \citet{madec.delecluse.ea_JPO96}: (\np[=.true.]{ln_dynhpg_sco}{ln\_dynhpg\_sco}) 
    668670\begin{equation} 
    669671  \label{eq:DYN_hpg_sco} 
     
    683685($e_{3w}$). 
    684686 
    685 $\bullet$ Traditional coding with adaptation for ice shelf cavities (\np{ln_dynhpg_isf}{ln\_dynhpg\_isf}\forcode{=.true.}). 
    686 This scheme need the activation of ice shelf cavities (\np{ln_isfcav}{ln\_isfcav}\forcode{=.true.}). 
    687  
    688 $\bullet$ Pressure Jacobian scheme (prj) (a research paper in preparation) (\np{ln_dynhpg_prj}{ln\_dynhpg\_prj}\forcode{=.true.}) 
     687$\bullet$ Traditional coding with adaptation for ice shelf cavities (\np[=.true.]{ln_dynhpg_isf}{ln\_dynhpg\_isf}). 
     688This scheme need the activation of ice shelf cavities (\np[=.true.]{ln_isfcav}{ln\_isfcav}). 
     689 
     690$\bullet$ Pressure Jacobian scheme (prj) (a research paper in preparation) (\np[=.true.]{ln_dynhpg_prj}{ln\_dynhpg\_prj}) 
    689691 
    690692$\bullet$ Density Jacobian with cubic polynomial scheme (DJC) \citep{shchepetkin.mcwilliams_OM05} 
    691 (\np{ln_dynhpg_djc}{ln\_dynhpg\_djc}\forcode{=.true.}) (currently disabled; under development) 
     693(\np[=.true.]{ln_dynhpg_djc}{ln\_dynhpg\_djc}) (currently disabled; under development) 
    692694 
    693695Note that expression \autoref{eq:DYN_hpg_sco} is commonly used when the variable volume formulation is activated 
    694696(\texttt{vvl?}) because in that case, even with a flat bottom, 
    695697the coordinate surfaces are not horizontal but follow the free surface \citep{levier.treguier.ea_rpt07}. 
    696 The pressure jacobian scheme (\np{ln_dynhpg_prj}{ln\_dynhpg\_prj}\forcode{=.true.}) is available as 
    697 an improved option to \np{ln_dynhpg_sco}{ln\_dynhpg\_sco}\forcode{=.true.} when \texttt{vvl?} is active. 
     698The pressure jacobian scheme (\np[=.true.]{ln_dynhpg_prj}{ln\_dynhpg\_prj}) is available as 
     699an improved option to \np[=.true.]{ln_dynhpg_sco}{ln\_dynhpg\_sco} when \texttt{vvl?} is active. 
    698700The pressure Jacobian scheme uses a constrained cubic spline to 
    699701reconstruct the density profile across the water column. 
     
    707709 
    708710Beneath an ice shelf, the total pressure gradient is the sum of the pressure gradient due to the ice shelf load and 
    709 the pressure gradient due to the ocean load (\np{ln_dynhpg_isf}{ln\_dynhpg\_isf}\forcode{=.true.}).\\ 
     711the pressure gradient due to the ocean load (\np[=.true.]{ln_dynhpg_isf}{ln\_dynhpg\_isf}).\\ 
    710712 
    711713The main hypothesis to compute the ice shelf load is that the ice shelf is in an isostatic equilibrium. 
     
    738740rather than at the central time level $t$ only, as in the standard leapfrog scheme. 
    739741 
    740 $\bullet$ leapfrog scheme (\np{ln_dynhpg_imp}{ln\_dynhpg\_imp}\forcode{=.true.}): 
     742$\bullet$ leapfrog scheme (\np[=.true.]{ln_dynhpg_imp}{ln\_dynhpg\_imp}): 
    741743 
    742744\begin{equation} 
     
    746748\end{equation} 
    747749 
    748 $\bullet$ semi-implicit scheme (\np{ln_dynhpg_imp}{ln\_dynhpg\_imp}\forcode{=.true.}): 
     750$\bullet$ semi-implicit scheme (\np[=.true.]{ln_dynhpg_imp}{ln\_dynhpg\_imp}): 
    749751\begin{equation} 
    750752  \label{eq:DYN_hpg_imp} 
     
    764766such as the stability limits associated with advection or diffusion. 
    765767 
    766 In practice, the semi-implicit scheme is used when \np{ln_dynhpg_imp}{ln\_dynhpg\_imp}\forcode{=.true.}. 
     768In practice, the semi-implicit scheme is used when \np[=.true.]{ln_dynhpg_imp}{ln\_dynhpg\_imp}. 
    767769In this case, we choose to apply the time filter to temperature and salinity used in the equation of state, 
    768770instead of applying it to the hydrostatic pressure or to the density, 
     
    865867The size of the small time step, $\rdt_e$ (the external mode or barotropic time step) is provided through 
    866868the \np{nn_baro}{nn\_baro} namelist parameter as: $\rdt_e = \rdt / nn\_baro$. 
    867 This parameter can be optionally defined automatically (\np{ln_bt_nn_auto}{ln\_bt\_nn\_auto}\forcode{=.true.}) considering that 
     869This parameter can be optionally defined automatically (\np[=.true.]{ln_bt_nn_auto}{ln\_bt\_nn\_auto}) considering that 
    868870the stability of the barotropic system is essentially controled by external waves propagation. 
    869871Maximum Courant number is in that case time independent, and easily computed online from the input bathymetry. 
     
    904906    In this particular exemple, 
    905907    a boxcar averaging window over \np{nn_baro}{nn\_baro} barotropic time steps is used 
    906     (\np{nn_bt_flt}{nn\_bt\_flt}\forcode{=1}) and \np{nn_baro}{nn\_baro}\forcode{=5}. 
     908    (\np[=1]{nn_bt_flt}{nn\_bt\_flt}) and \np[=5]{nn_baro}{nn\_baro}. 
    907909    Internal mode time steps (which are also the model time steps) are denoted by 
    908910    $t-\rdt$, $t$ and $t+\rdt$. 
     
    913915    the latter are used to obtain time averaged transports to advect tracers. 
    914916    a) Forward time integration: 
    915     \protect\np{ln_bt_fw}{ln\_bt\_fw}\forcode{=.true.},  \protect\np{ln_bt_av}{ln\_bt\_av}\forcode{=.true.}. 
     917    \protect\np[=.true.]{ln_bt_fw}{ln\_bt\_fw},  \protect\np[=.true.]{ln_bt_av}{ln\_bt\_av}. 
    916918    b) Centred time integration: 
    917     \protect\np{ln_bt_fw}{ln\_bt\_fw}\forcode{=.false.}, \protect\np{ln_bt_av}{ln\_bt\_av}\forcode{=.true.}. 
     919    \protect\np[=.false.]{ln_bt_fw}{ln\_bt\_fw}, \protect\np[=.true.]{ln_bt_av}{ln\_bt\_av}. 
    918920    c) Forward time integration with no time filtering (POM-like scheme): 
    919     \protect\np{ln_bt_fw}{ln\_bt\_fw}\forcode{=.true.},  \protect\np{ln_bt_av}{ln\_bt\_av}\forcode{=.false.}.} 
     921    \protect\np[=.true.]{ln_bt_fw}{ln\_bt\_fw},  \protect\np[=.false.]{ln_bt_av}{ln\_bt\_av}.} 
    920922  \label{fig:DYN_spg_ts} 
    921923\end{figure} 
    922924%>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   > 
    923925 
    924 In the default case (\np{ln_bt_fw}{ln\_bt\_fw}\forcode{=.true.}), 
     926In the default case (\np[=.true.]{ln_bt_fw}{ln\_bt\_fw}), 
    925927the external mode is integrated between \textit{now} and \textit{after} baroclinic time-steps 
    926928(\autoref{fig:DYN_spg_ts}a). 
    927929To avoid aliasing of fast barotropic motions into three dimensional equations, 
    928 time filtering is eventually applied on barotropic quantities (\np{ln_bt_av}{ln\_bt\_av}\forcode{=.true.}). 
     930time filtering is eventually applied on barotropic quantities (\np[=.true.]{ln_bt_av}{ln\_bt\_av}). 
    929931In that case, the integration is extended slightly beyond \textit{after} time step to 
    930932provide time filtered quantities. 
     
    933935asselin filtering is not applied to barotropic quantities.\\ 
    934936Alternatively, one can choose to integrate barotropic equations starting from \textit{before} time step 
    935 (\np{ln_bt_fw}{ln\_bt\_fw}\forcode{=.false.}). 
     937(\np[=.false.]{ln_bt_fw}{ln\_bt\_fw}). 
    936938Although more computationaly expensive ( \np{nn_baro}{nn\_baro} additional iterations are indeed necessary), 
    937939the baroclinic to barotropic forcing term given at \textit{now} time step become centred in 
     
    958960 
    959961One can eventually choose to feedback instantaneous values by not using any time filter 
    960 (\np{ln_bt_av}{ln\_bt\_av}\forcode{=.false.}). 
     962(\np[=.false.]{ln_bt_av}{ln\_bt\_av}). 
    961963In that case, external mode equations are continuous in time, 
    962964\ie\ they are not re-initialized when starting a new sub-stepping sequence. 
     
    11911193 
    11921194A rotation of the lateral momentum diffusion operator is needed in several cases: 
    1193 for iso-neutral diffusion in the $z$-coordinate (\np{ln_dynldf_iso}{ln\_dynldf\_iso}\forcode{=.true.}) and 
    1194 for either iso-neutral (\np{ln_dynldf_iso}{ln\_dynldf\_iso}\forcode{=.true.}) or 
    1195 geopotential (\np{ln_dynldf_hor}{ln\_dynldf\_hor}\forcode{=.true.}) diffusion in the $s$-coordinate. 
     1195for iso-neutral diffusion in the $z$-coordinate (\np[=.true.]{ln_dynldf_iso}{ln\_dynldf\_iso}) and 
     1196for either iso-neutral (\np[=.true.]{ln_dynldf_iso}{ln\_dynldf\_iso}) or 
     1197geopotential (\np[=.true.]{ln_dynldf_hor}{ln\_dynldf\_hor}) diffusion in the $s$-coordinate. 
    11961198In the partial step case, coordinates are horizontal except at the deepest level and 
    1197 no rotation is performed when \np{ln_dynldf_hor}{ln\_dynldf\_hor}\forcode{=.true.}. 
     1199no rotation is performed when \np[=.true.]{ln_dynldf_hor}{ln\_dynldf\_hor}. 
    11981200The diffusion operator is defined simply as the divergence of down gradient momentum fluxes on 
    11991201each momentum component. 
     
    12691271Two time stepping schemes can be used for the vertical diffusion term: 
    12701272$(a)$ a forward time differencing scheme 
    1271 (\np{ln_zdfexp}{ln\_zdfexp}\forcode{=.true.}) using a time splitting technique (\np{nn_zdfexp}{nn\_zdfexp} $>$ 1) or 
    1272 $(b)$ a backward (or implicit) time differencing scheme (\np{ln_zdfexp}{ln\_zdfexp}\forcode{=.false.}) 
     1273(\np[=.true.]{ln_zdfexp}{ln\_zdfexp}) using a time splitting technique (\np{nn_zdfexp}{nn\_zdfexp} $>$ 1) or 
     1274$(b)$ a backward (or implicit) time differencing scheme (\np[=.false.]{ln_zdfexp}{ln\_zdfexp}) 
    12731275(see \autoref{chap:TD}). 
    12741276Note that namelist variables \np{ln_zdfexp}{ln\_zdfexp} and \np{nn_zdfexp}{nn\_zdfexp} apply to both tracers and dynamics. 
     
    13201322three other forcings may enter the dynamical equations by affecting the surface pressure gradient. 
    13211323 
    1322 (1) When \np{ln_apr_dyn}{ln\_apr\_dyn}\forcode{=.true.} (see \autoref{sec:SBC_apr}), 
     1324(1) When \np[=.true.]{ln_apr_dyn}{ln\_apr\_dyn} (see \autoref{sec:SBC_apr}), 
    13231325the atmospheric pressure is taken into account when computing the surface pressure gradient. 
    13241326 
    1325 (2) When \np{ln_tide_pot}{ln\_tide\_pot}\forcode{=.true.} and \np{ln_tide}{ln\_tide}\forcode{=.true.} (see \autoref{sec:SBC_tide}), 
     1327(2) When \np[=.true.]{ln_tide_pot}{ln\_tide\_pot} and \np[=.true.]{ln_tide}{ln\_tide} (see \autoref{sec:SBC_tide}), 
    13261328the tidal potential is taken into account when computing the surface pressure gradient. 
    13271329 
    1328 (3) When \np{nn_ice_embd}{nn\_ice\_embd}\forcode{=2} and LIM or CICE is used 
     1330(3) When \np[=2]{nn_ice_embd}{nn\_ice\_embd} and LIM or CICE is used 
    13291331(\ie\ when the sea-ice is embedded in the ocean), 
    13301332the snow-ice mass is taken into account when computing the surface pressure gradient. 
     
    14061408 
    14071409The flux across each $u$-face of a tracer cell is multiplied by a factor zuwdmask (an array which depends on ji and jj). 
    1408 If the user sets \np{ln_wd_dl_ramp}{ln\_wd\_dl\_ramp}\forcode{=.false.} then zuwdmask is 1 when the 
     1410If the user sets \np[=.false.]{ln_wd_dl_ramp}{ln\_wd\_dl\_ramp} then zuwdmask is 1 when the 
    14091411flux is from a cell with water depth greater than \np{rn_wdmin1}{rn\_wdmin1} and 0 otherwise. If the user sets 
    1410 \np{ln_wd_dl_ramp}{ln\_wd\_dl\_ramp}\forcode{=.true.} the flux across the face is ramped down as the water depth decreases 
     1412\np[=.true.]{ln_wd_dl_ramp}{ln\_wd\_dl\_ramp} the flux across the face is ramped down as the water depth decreases 
    14111413from 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. 
    14121414 
     
    14251427fields (tracers independent of $x$, $y$ and $z$). Our scheme conserves constant tracers because 
    14261428the velocities used at the tracer cell faces on the baroclinic timesteps are carefully calculated by dynspg\_ts 
    1427 to equal their mean value during the barotropic steps. If the user sets \np{ln_wd_dl_bc}{ln\_wd\_dl\_bc}\forcode{=.true.}, the 
     1429to equal their mean value during the barotropic steps. If the user sets \np[=.true.]{ln_wd_dl_bc}{ln\_wd\_dl\_bc}, the 
    14281430baroclinic velocities are also multiplied by a suitably weighted average of zuwdmask. 
    14291431 
     
    16581660 
    16591661$\bullet$ vector invariant form or linear free surface 
    1660 (\np{ln_dynhpg_vec}{ln\_dynhpg\_vec}\forcode{=.true.} ; \texttt{vvl?} not defined): 
     1662(\np[=.true.]{ln_dynhpg_vec}{ln\_dynhpg\_vec} ; \texttt{vvl?} not defined): 
    16611663\[ 
    16621664  % \label{eq:DYN_nxt_vec} 
     
    16701672 
    16711673$\bullet$ flux form and nonlinear free surface 
    1672 (\np{ln_dynhpg_vec}{ln\_dynhpg\_vec}\forcode{=.false.} ; \texttt{vvl?} defined): 
     1674(\np[=.false.]{ln_dynhpg_vec}{ln\_dynhpg\_vec} ; \texttt{vvl?} defined): 
    16731675\[ 
    16741676  % \label{eq:DYN_nxt_flux} 
     
    16841686the subscript $f$ denotes filtered values and $\gamma$ is the Asselin coefficient. 
    16851687$\gamma$ is initialized as \np{nn_atfp}{nn\_atfp} (namelist parameter). 
    1686 Its default value is \np{nn_atfp}{nn\_atfp}\forcode{=10.e-3}. 
     1688Its default value is \np[=10.e-3]{nn_atfp}{nn\_atfp}. 
    16871689In both cases, the modified Asselin filter is not applied since perfect conservation is not an issue for 
    16881690the momentum equations. 
     
    16931695 
    16941696% ================================================================ 
    1695 \biblio 
    1696  
    1697 \pindex 
     1697\onlyinsubfile{\bibliography{../main/bibliography}} 
     1698 
     1699\onlyinsubfile{\printindex} 
    16981700 
    16991701\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex

    r11578 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    101103  \caption[Lateral boundary conditions]{ 
    102104    Lateral boundary conditions 
    103     (a) free-slip                       (\protect\np{rn_shlat}{rn\_shlat}\forcode{=0}); 
    104     (b) no-slip                         (\protect\np{rn_shlat}{rn\_shlat}\forcode{=2}); 
    105     (c) "partial" free-slip (\forcode{0<}\protect\np{rn_shlat}{rn\_shlat}\forcode{<2}) and 
     105    (a) free-slip                       (\protect\np[=0]{rn_shlat}{rn\_shlat}); 
     106    (b) no-slip                         (\protect\np[=2]{rn_shlat}{rn\_shlat}); 
     107    (c) "partial" free-slip (\forcode{0<}\protect\np[<2]{rn_shlat}{rn\_shlat}) and 
    106108    (d) "strong" no-slip    (\forcode{2<}\protect\np{rn_shlat}{rn\_shlat}). 
    107109    Implied "ghost" velocity inside land area is display in grey.} 
     
    112114\begin{description} 
    113115 
    114 \item[free-slip boundary condition (\np{rn_shlat}{rn\_shlat}\forcode{=0}):] the tangential velocity at 
     116\item[free-slip boundary condition ({\np[=0]{rn_shlat}{rn\_shlat}})] the tangential velocity at 
    115117  the coastline is equal to the offshore velocity, 
    116118  \ie\ the normal derivative of the tangential velocity is zero at the coast, 
     
    118120  (\autoref{fig:LBC_shlat}-a). 
    119121 
    120 \item[no-slip boundary condition (\np{rn_shlat}{rn\_shlat}\forcode{=2}):] the tangential velocity vanishes at the coastline. 
     122\item[no-slip boundary condition ({\np[=2]{rn_shlat}{rn\_shlat}})] the tangential velocity vanishes at the coastline. 
    121123  Assuming that the tangential velocity decreases linearly from 
    122124  the closest ocean velocity grid point to the coastline, 
     
    139141  \] 
    140142 
    141 \item["partial" free-slip boundary condition (0$<$\np{rn_shlat}{rn\_shlat}$<$2):] the tangential velocity at 
     143\item["partial" free-slip boundary condition (0$<$\np{rn_shlat}{rn\_shlat}$<$2)] the tangential velocity at 
    142144  the coastline is smaller than the offshore velocity, \ie\ there is a lateral friction but 
    143145  not strong enough to make the tangential velocity at the coast vanish (\autoref{fig:LBC_shlat}-c). 
    144146  This can be selected by providing a value of mask$_{f}$ strictly inbetween $0$ and $2$. 
    145147 
    146 \item["strong" no-slip boundary condition (2$<$\np{rn_shlat}{rn\_shlat}):] the viscous boundary layer is assumed to 
     148\item["strong" no-slip boundary condition (2$<$\np{rn_shlat}{rn\_shlat})] the viscous boundary layer is assumed to 
    147149  be smaller than half the grid size (\autoref{fig:LBC_shlat}-d). 
    148150  The friction is thus larger than in the no-slip case. 
     
    393395\label{subsec:LBC_bdy_namelist} 
    394396 
    395 The BDY module is activated by setting \np{ln_bdy}{ln\_bdy}\forcode{=.true.} . 
     397The BDY module is activated by setting \np[=.true.]{ln_bdy}{ln\_bdy} . 
    396398It is possible to define more than one boundary ``set'' and apply different boundary conditions to each set. 
    397399The number of boundary sets is defined by \np{nb_bdy}{nb\_bdy}. 
    398400Each boundary set can be either defined as a series of straight line segments directly in the namelist 
    399 (\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). 
     401(\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). 
    400402The coordinates.bdy file is analagous to the usual \NEMO\ ``\ifile{coordinates}'' file. 
    401403In the example above, there are two boundary sets, the first of which is defined via a file and 
     
    422424 
    423425The boundary data is either set to initial conditions 
    424 (\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}). 
     426(\np[=0]{nn_tra_dta}{nn\_tra\_dta}) or forced with external data from a file (\np[=1]{nn_tra_dta}{nn\_tra\_dta}). 
    425427In case the 3d velocity data contain the total velocity (ie, baroclinic and barotropic velocity), 
    426 the bdy code can derived baroclinic and barotropic velocities by setting \np{ln_full_vel}{ln\_full\_vel}\forcode{=.true.} 
     428the bdy code can derived baroclinic and barotropic velocities by setting \np[=.true.]{ln_full_vel}{ln\_full\_vel} 
    427429For the barotropic solution there is also the option to use tidal harmonic forcing either by 
    428 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}).\\ 
     430itself (\np[=2]{nn_dyn2d_dta}{nn\_dyn2d\_dta}) or in addition to other external data (\np[=3]{nn_dyn2d_dta}{nn\_dyn2d\_dta}).\\ 
    429431If 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}. 
    430432 
     
    602604\jp{jpinft} give the start and end $i$ indices for each segment with similar for the other boundaries. 
    603605These segments define a list of $T$ grid points along the outermost row of the boundary ($nbr\,=\, 1$). 
    604 The code deduces the $U$ and $V$ points and also the points for $nbr\,>\, 1$ if \np{nn_rimwidth}{nn\_rimwidth}\forcode{>1}. 
     606The code deduces the $U$ and $V$ points and also the points for $nbr\,>\, 1$ if \np[>1]{nn_rimwidth}{nn\_rimwidth}. 
    605607 
    606608The boundary geometry may also be defined from a ``\ifile{coordinates.bdy}'' file. 
     
    673675There is an option to force the total volume in the regional model to be constant. 
    674676This is controlled  by the \np{ln_vol}{ln\_vol} parameter in the namelist. 
    675 A value of \np{ln_vol}{ln\_vol}\forcode{=.false.} indicates that this option is not used. 
     677A value of \np[=.false.]{ln_vol}{ln\_vol} indicates that this option is not used. 
    676678Two options to control the volume are available (\np{nn_volctl}{nn\_volctl}). 
    677 If \np{nn_volctl}{nn\_volctl}\forcode{=0} then a correction is applied to the normal barotropic velocities around the boundary at 
     679If \np[=0]{nn_volctl}{nn\_volctl} then a correction is applied to the normal barotropic velocities around the boundary at 
    678680each timestep to ensure that the integrated volume flow through the boundary is zero. 
    679 If \np{nn_volctl}{nn\_volctl}\forcode{=1} then the calculation of the volume change on 
     681If \np[=1]{nn_volctl}{nn\_volctl} then the calculation of the volume change on 
    680682the timestep includes the change due to the freshwater flux across the surface and 
    681683the correction velocity corrects for this as well. 
     
    741743direction of rotation). %, e.g. anticlockwise or clockwise. 
    742744 
    743 \biblio 
    744  
    745 \pindex 
     745\onlyinsubfile{\bibliography{../main/bibliography}} 
     746 
     747\onlyinsubfile{\printindex} 
    746748 
    747749\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex

    r11578 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    2426(see the \nam{tra_ldf}{tra\_ldf} and \nam{dyn_ldf}{dyn\_ldf} below). 
    2527Note that this chapter describes the standard implementation of iso-neutral tracer mixing. 
    26 Griffies's implementation, which is used if \np{ln_traldf_triad}{ln\_traldf\_triad}\forcode{=.true.}, 
     28Griffies's implementation, which is used if \np[=.true.]{ln_traldf_triad}{ln\_traldf\_triad}, 
    2729is described in \autoref{apdx:TRIADS} 
    2830 
     
    4042\subsection[No lateral mixing (\forcode{ln_traldf_OFF} \& \forcode{ln_dynldf_OFF})]{No lateral mixing (\protect\np{ln_traldf_OFF}{ln\_traldf\_OFF} \& \protect\np{ln_dynldf_OFF}{ln\_dynldf\_OFF})} 
    4143 
    42 It is possible to run without explicit lateral diffusion on tracers (\protect\np{ln_traldf_OFF}{ln\_traldf\_OFF}\forcode{=.true.}) and/or 
    43 momentum (\protect\np{ln_dynldf_OFF}{ln\_dynldf\_OFF}\forcode{=.true.}). The latter option is even recommended if using the 
    44 UBS advection scheme on momentum (\np{ln_dynadv_ubs}{ln\_dynadv\_ubs}\forcode{=.true.}, 
     44It is possible to run without explicit lateral diffusion on tracers (\protect\np[=.true.]{ln_traldf_OFF}{ln\_traldf\_OFF}) and/or 
     45momentum (\protect\np[=.true.]{ln_dynldf_OFF}{ln\_dynldf\_OFF}). The latter option is even recommended if using the 
     46UBS advection scheme on momentum (\np[=.true.]{ln_dynadv_ubs}{ln\_dynadv\_ubs}, 
    4547see \autoref{subsec:DYN_adv_ubs}) and can be useful for testing purposes. 
    4648 
    4749\subsection[Laplacian mixing (\forcode{ln_traldf_lap} \& \forcode{ln_dynldf_lap})]{Laplacian mixing (\protect\np{ln_traldf_lap}{ln\_traldf\_lap} \& \protect\np{ln_dynldf_lap}{ln\_dynldf\_lap})} 
    48 Setting \protect\np{ln_traldf_lap}{ln\_traldf\_lap}\forcode{=.true.} and/or \protect\np{ln_dynldf_lap}{ln\_dynldf\_lap}\forcode{=.true.} enables 
     50Setting \protect\np[=.true.]{ln_traldf_lap}{ln\_traldf\_lap} and/or \protect\np[=.true.]{ln_dynldf_lap}{ln\_dynldf\_lap} enables 
    4951a second order diffusion on tracers and momentum respectively. Note that in \NEMO\ 4, one can not combine 
    5052Laplacian and Bilaplacian operators for the same variable. 
    5153 
    5254\subsection[Bilaplacian mixing (\forcode{ln_traldf_blp} \& \forcode{ln_dynldf_blp})]{Bilaplacian mixing (\protect\np{ln_traldf_blp}{ln\_traldf\_blp} \& \protect\np{ln_dynldf_blp}{ln\_dynldf\_blp})} 
    53 Setting \protect\np{ln_traldf_blp}{ln\_traldf\_blp}\forcode{=.true.} and/or \protect\np{ln_dynldf_blp}{ln\_dynldf\_blp}\forcode{=.true.} enables 
     55Setting \protect\np[=.true.]{ln_traldf_blp}{ln\_traldf\_blp} and/or \protect\np[=.true.]{ln_dynldf_blp}{ln\_dynldf\_blp} enables 
    5456a fourth order diffusion on tracers and momentum respectively. It is implemented by calling the above Laplacian operator twice. 
    5557We stress again that from \NEMO\ 4, the simultaneous use Laplacian and Bilaplacian operators is not allowed. 
     
    107109%gm%  caution I'm not sure the simplification was a good idea! 
    108110 
    109 These slopes are computed once in \rou{ldf\_slp\_init} when \np{ln_sco}{ln\_sco}\forcode{=.true.}, 
    110 and either \np{ln_traldf_hor}{ln\_traldf\_hor}\forcode{=.true.} or \np{ln_dynldf_hor}{ln\_dynldf\_hor}\forcode{=.true.}. 
     111These slopes are computed once in \rou{ldf\_slp\_init} when \np[=.true.]{ln_sco}{ln\_sco}, 
     112and either \np[=.true.]{ln_traldf_hor}{ln\_traldf\_hor} or \np[=.true.]{ln_dynldf_hor}{ln\_dynldf\_hor}. 
    111113 
    112114\subsection{Slopes for tracer iso-neutral mixing} 
     
    164166\item[$s$- or hybrid $s$-$z$- coordinate: ] 
    165167  in the current release of \NEMO, iso-neutral mixing is only employed for $s$-coordinates if 
    166   the Griffies scheme is used (\np{ln_traldf_triad}{ln\_traldf\_triad}\forcode{=.true.}; 
     168  the Griffies scheme is used (\np[=.true.]{ln_traldf_triad}{ln\_traldf\_triad}; 
    167169  see \autoref{apdx:TRIADS}). 
    168170  In other words, iso-neutral mixing will only be accurately represented with a linear equation of state 
    169   (\np{ln_seos}{ln\_seos}\forcode{=.true.}). 
     171  (\np[=.true.]{ln_seos}{ln\_seos}). 
    170172  In the case of a "true" equation of state, the evaluation of $i$ and $j$ derivatives in \autoref{eq:LDF_slp_iso} 
    171173  will include a pressure dependent part, leading to the wrong evaluation of the neutral slopes. 
     
    222224To overcome this problem, several techniques have been proposed in which the numerical schemes of 
    223225the ocean model are modified \citep{weaver.eby_JPO97, griffies.gnanadesikan.ea_JPO98}. 
    224 Griffies's scheme is now available in \NEMO\ if \np{ln_traldf_triad}{ln\_traldf\_triad}\forcode{ = .true.}; see \autoref{apdx:TRIADS}. 
     226Griffies's scheme is now available in \NEMO\ if \np[=.true.]{ln_traldf_triad}{ln\_traldf\_triad}; see \autoref{apdx:TRIADS}. 
    225227Here, another strategy is presented \citep{lazar_phd97}: 
    226228a local filtering of the iso-neutral slopes (made on 9 grid-points) prevents the development of 
     
    326328The way the mixing coefficients are set in the reference version can be described as follows: 
    327329 
    328 \subsection[Mixing coefficients read from file (\forcode{=-20, -30})]{ Mixing coefficients read from file (\protect\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=-20, -30} \& \protect\np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=-20, -30})} 
     330\subsection[Mixing coefficients read from file (\forcode{=-20, -30})]{ Mixing coefficients read from file (\protect\np[=-20, -30]{nn_aht_ijk_t}{nn\_aht\_ijk\_t} \& \protect\np[=-20, -30]{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t})} 
    329331 
    330332Mixing coefficients can be read from file if a particular geographical variation is needed. For example, in the ORCA2 global ocean model, 
     
    332334decreases linearly to $A^l$~= 2.10$^3$ m$^2$/s at the equator \citep{madec.delecluse.ea_JPO96, delecluse.madec_icol99}. 
    333335Similar modified horizontal variations can be found with the Antarctic or Arctic sub-domain options of ORCA2 and ORCA05. 
    334 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}). 
     336The provided fields can either be 2d (\np[=-20]{nn_aht_ijk_t}{nn\_aht\_ijk\_t}, \np[=-20]{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}) or 3d (\np[=-30]{nn_aht_ijk_t}{nn\_aht\_ijk\_t},  \np[=-30]{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}). They must be given at U, V points for tracers and T, F points for momentum (see \autoref{tab:LDF_files}). 
    335337 
    336338%-------------------------------------------------TABLE--------------------------------------------------- 
     
    340342    \hline 
    341343    Namelist parameter                       & Input filename                               & dimensions & variable names                      \\  \hline 
    342     \np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=-20}      & \forcode{eddy_viscosity_2D.nc }            &     $(i,j)$         & \forcode{ahmt_2d, ahmf_2d}  \\  \hline 
    343     \np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=-20}           & \forcode{eddy_diffusivity_2D.nc }           &     $(i,j)$         & \forcode{ahtu_2d, ahtv_2d}    \\   \hline 
    344     \np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=-30}      & \forcode{eddy_viscosity_3D.nc }            &     $(i,j,k)$          & \forcode{ahmt_3d, ahmf_3d}  \\  \hline 
    345     \np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=-30}      & \forcode{eddy_diffusivity_3D.nc }           &     $(i,j,k)$         & \forcode{ahtu_3d, ahtv_3d}    \\   \hline 
     344    \np[=-20]{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}     & \forcode{eddy_viscosity_2D.nc }            &     $(i,j)$         & \forcode{ahmt_2d, ahmf_2d}  \\  \hline 
     345    \np[=-20]{nn_aht_ijk_t}{nn\_aht\_ijk\_t}           & \forcode{eddy_diffusivity_2D.nc }           &     $(i,j)$           & \forcode{ahtu_2d, ahtv_2d}    \\   \hline 
     346    \np[=-30]{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}        & \forcode{eddy_viscosity_3D.nc }            &     $(i,j,k)$          & \forcode{ahmt_3d, ahmf_3d}  \\  \hline 
     347    \np[=-30]{nn_aht_ijk_t}{nn\_aht\_ijk\_t}     & \forcode{eddy_diffusivity_3D.nc }           &     $(i,j,k)$         & \forcode{ahtu_3d, ahtv_3d}    \\   \hline 
    346348  \end{tabular} 
    347349  \caption{Description of expected input files if mixing coefficients are read from NetCDF files} 
     
    350352%-------------------------------------------------------------------------------------------------------------- 
    351353 
    352 \subsection[Constant mixing coefficients (\forcode{=0})]{ Constant mixing coefficients (\protect\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=0} \& \protect\np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=0})} 
     354\subsection[Constant mixing coefficients (\forcode{=0})]{ Constant mixing coefficients (\protect\np[=0]{nn_aht_ijk_t}{nn\_aht\_ijk\_t} \& \protect\np[=0]{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t})} 
    353355 
    354356If constant, mixing coefficients are set thanks to a velocity and a length scales ($U_{scl}$, $L_{scl}$) such that: 
     
    366368 $U_{scl}$ and $L_{scl}$ are given by the namelist parameters \np{rn_Ud}{rn\_Ud}, \np{rn_Uv}{rn\_Uv}, \np{rn_Ld}{rn\_Ld} and \np{rn_Lv}{rn\_Lv}. 
    367369 
    368 \subsection[Vertically varying mixing coefficients (\forcode{=10})]{Vertically varying mixing coefficients (\protect\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=10} \& \protect\np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=10})} 
     370\subsection[Vertically varying mixing coefficients (\forcode{=10})]{Vertically varying mixing coefficients (\protect\np[=10]{nn_aht_ijk_t}{nn\_aht\_ijk\_t} \& \protect\np[=10]{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t})} 
    369371 
    370372In the vertically varying case, a hyperbolic variation of the lateral mixing coefficient is introduced in which 
     
    373375This profile is hard coded in module \mdl{ldfc1d\_c2d}, but can be easily modified by users. 
    374376 
    375 \subsection[Mesh size dependent mixing coefficients (\forcode{=20})]{Mesh size dependent mixing coefficients (\protect\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=20} \& \protect\np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=20})} 
     377\subsection[Mesh size dependent mixing coefficients (\forcode{=20})]{Mesh size dependent mixing coefficients (\protect\np[=20]{nn_aht_ijk_t}{nn\_aht\_ijk\_t} \& \protect\np[=20]{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t})} 
    376378 
    377379In that case, the horizontal variation of the eddy coefficient depends on the local mesh size and 
     
    398400\colorbox{yellow}{CASE \np{nn_aht_ijk_t}{nn\_aht\_ijk\_t} = 21 to be added} 
    399401 
    400 \subsection[Mesh size and depth dependent mixing coefficients (\forcode{=30})]{Mesh size and depth dependent mixing coefficients (\protect\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=30} \& \protect\np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=30})} 
     402\subsection[Mesh size and depth dependent mixing coefficients (\forcode{=30})]{Mesh size and depth dependent mixing coefficients (\protect\np[=30]{nn_aht_ijk_t}{nn\_aht\_ijk\_t} \& \protect\np[=30]{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t})} 
    401403 
    402404The 3D space variation of the mixing coefficient is simply the combination of the 1D and 2D cases above, 
     
    404406the magnitude of the coefficient. 
    405407 
    406 \subsection[Velocity dependent mixing coefficients (\forcode{=31})]{Flow dependent mixing coefficients (\protect\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=31} \& \protect\np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=31})} 
     408\subsection[Velocity dependent mixing coefficients (\forcode{=31})]{Flow dependent mixing coefficients (\protect\np[=31]{nn_aht_ijk_t}{nn\_aht\_ijk\_t} \& \protect\np[=31]{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t})} 
    407409In that case, the eddy coefficient is proportional to the local velocity magnitude so that the Reynolds number $Re =  \lvert U \rvert  e / A_l$ is constant (and here hardcoded to $12$): 
    408410\colorbox{yellow}{JC comment: The Reynolds is effectively set to 12 in the code for both operators but shouldn't it be 2 for Laplacian ?} 
     
    418420\end{equation} 
    419421 
    420 \subsection[Deformation rate dependent viscosities (\forcode{nn_ahm_ijk_t=32})]{Deformation rate dependent viscosities (\protect\np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=32})} 
     422\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})} 
    421423 
    422424This option refers to the \citep{smagorinsky_MW63} scheme which is here implemented for momentum only. Smagorinsky chose as a 
     
    505507} 
    506508 
    507 When  \citet{gent.mcwilliams_JPO90} diffusion is used (\np{ln_ldfeiv}{ln\_ldfeiv}\forcode{=.true.}), 
     509When  \citet{gent.mcwilliams_JPO90} diffusion is used (\np[=.true.]{ln_ldfeiv}{ln\_ldfeiv}), 
    508510an eddy induced tracer advection term is added, 
    509511the formulation of which depends on the slopes of iso-neutral surfaces. 
     
    512514and the sum \autoref{eq:LDF_slp_geo} + \autoref{eq:LDF_slp_iso} in $s$-coordinates. 
    513515 
    514 If isopycnal mixing is used in the standard way, \ie\ \np{ln_traldf_triad}{ln\_traldf\_triad}\forcode{=.false.}, the eddy induced velocity is given by: 
     516If isopycnal mixing is used in the standard way, \ie\ \np[=.false.]{ln_traldf_triad}{ln\_traldf\_triad}, the eddy induced velocity is given by: 
    515517\begin{equation} 
    516518  \label{eq:LDF_eiv} 
     
    536538\colorbox{yellow}{CASE \np{nn_aei_ijk_t}{nn\_aei\_ijk\_t} = 21 to be added} 
    537539 
    538 In case of setting \np{ln_traldf_triad}{ln\_traldf\_triad}\forcode{ = .true.}, a skew form of the eddy induced advective fluxes is used, which is described in \autoref{apdx:TRIADS}. 
     540In case of setting \np[=.true.]{ln_traldf_triad}{ln\_traldf\_triad}, a skew form of the eddy induced advective fluxes is used, which is described in \autoref{apdx:TRIADS}. 
    539541 
    540542% ================================================================ 
     
    554556%-------------------------------------------------------------------------------------------------------------- 
    555557 
    556 If  \np{ln_mle}{ln\_mle}\forcode{=.true.} 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. 
     558If  \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. 
    557559 
    558560\colorbox{yellow}{TBC} 
    559561 
    560 \biblio 
    561  
    562 \pindex 
     562\onlyinsubfile{\bibliography{../main/bibliography}} 
     563 
     564\onlyinsubfile{\printindex} 
    563565 
    564566\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_OBS.tex

    r11578 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    569571Values between 0 to 4 are associated with interpolation while values 5 or 6 are associated with averaging. 
    570572\begin{itemize} 
    571 \item \np{nn_2dint}{nn\_2dint}\forcode{ = 0}: Distance-weighted interpolation 
    572 \item \np{nn_2dint}{nn\_2dint}\forcode{ = 1}: Distance-weighted interpolation (small angle) 
    573 \item \np{nn_2dint}{nn\_2dint}\forcode{ = 2}: Bilinear interpolation (geographical grid) 
    574 \item \np{nn_2dint}{nn\_2dint}\forcode{ = 3}: Bilinear remapping interpolation (general grid) 
    575 \item \np{nn_2dint}{nn\_2dint}\forcode{ = 4}: Polynomial interpolation 
    576 \item \np{nn_2dint}{nn\_2dint}\forcode{ = 5}: Radial footprint averaging with diameter specified in the namelist as 
     573\item \np[=0]{nn_2dint}{nn\_2dint}: Distance-weighted interpolation 
     574\item \np[=1]{nn_2dint}{nn\_2dint}: Distance-weighted interpolation (small angle) 
     575\item \np[=2]{nn_2dint}{nn\_2dint}: Bilinear interpolation (geographical grid) 
     576\item \np[=3]{nn_2dint}{nn\_2dint}: Bilinear remapping interpolation (general grid) 
     577\item \np[=4]{nn_2dint}{nn\_2dint}: Polynomial interpolation 
     578\item \np[=5]{nn_2dint}{nn\_2dint}: Radial footprint averaging with diameter specified in the namelist as 
    577579  \texttt{rn\_[var]\_avglamscl} in degrees or metres (set using \texttt{ln\_[var]\_fp\_indegs}) 
    578 \item \np{nn_2dint}{nn\_2dint}\forcode{ = 6}: Rectangular footprint averaging with E/W and N/S size specified in 
     580\item \np[=6]{nn_2dint}{nn\_2dint}: Rectangular footprint averaging with E/W and N/S size specified in 
    579581  the namelist as \texttt{rn\_[var]\_avglamscl} and \texttt{rn\_[var]\_avgphiscl} in degrees or metres 
    580582  (set using \texttt{ln\_[var]\_fp\_indegs}) 
     
    11681170%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    11691171 
    1170 \biblio 
    1171  
    1172 \pindex 
     1172\onlyinsubfile{\bibliography{../main/bibliography}} 
     1173 
     1174\onlyinsubfile{\printindex} 
    11731175 
    11741176\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex

    r11578 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    4143\begin{itemize} 
    4244\item 
    43   a bulk formulation (\np{ln_blk}{ln\_blk}\forcode{=.true.} with four possible bulk algorithms), 
    44 \item 
    45   a flux formulation (\np{ln_flx}{ln\_flx}\forcode{=.true.}), 
     45  a bulk formulation (\np[=.true.]{ln_blk}{ln\_blk} with four possible bulk algorithms), 
     46\item 
     47  a flux formulation (\np[=.true.]{ln_flx}{ln\_flx}), 
    4648\item 
    4749  a coupled or mixed forced/coupled formulation (exchanges with a atmospheric model via the OASIS coupler), 
    48 (\np{ln_cpl}{ln\_cpl} or \np{ln_mixcpl}{ln\_mixcpl}\forcode{=.true.}), 
    49 \item 
    50   a user defined formulation (\np{ln_usr}{ln\_usr}\forcode{=.true.}). 
     50(\np{ln_cpl}{ln\_cpl} or \np[=.true.]{ln_mixcpl}{ln\_mixcpl}), 
     51\item 
     52  a user defined formulation (\np[=.true.]{ln_usr}{ln\_usr}). 
    5153\end{itemize} 
    5254 
     
    6971  the local grid directions in the model, 
    7072\item 
    71   the use of a land/sea mask for input fields (\np{nn_lsm}{nn\_lsm}\forcode{=.true.}), 
    72 \item 
    73   the addition of a surface restoring term to observed SST and/or SSS (\np{ln_ssr}{ln\_ssr}\forcode{=.true.}), 
     73  the use of a land/sea mask for input fields (\np[=.true.]{nn_lsm}{nn\_lsm}), 
     74\item 
     75  the addition of a surface restoring term to observed SST and/or SSS (\np[=.true.]{ln_ssr}{ln\_ssr}), 
    7476\item 
    7577  the modification of fluxes below ice-covered areas (using climatological ice-cover or a sea-ice model) 
    76   (\np{nn_ice}{nn\_ice}\forcode{=0..3}), 
    77 \item 
    78   the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np{ln_rnf}{ln\_rnf}\forcode{=.true.}), 
     78  (\np[=0..3]{nn_ice}{nn\_ice}), 
     79\item 
     80  the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np[=.true.]{ln_rnf}{ln\_rnf}), 
    7981\item 
    8082  the addition of ice-shelf melting as lateral inflow (parameterisation) or 
    81   as fluxes applied at the land-ice ocean interface (\np{ln_isf}{ln\_isf}\forcode{=.true.}), 
     83  as fluxes applied at the land-ice ocean interface (\np[=.true.]{ln_isf}{ln\_isf}), 
    8284\item 
    8385  the addition of a freshwater flux adjustment in order to avoid a mean sea-level drift 
    84   (\np{nn_fwb}{nn\_fwb}\forcode{=0..2}), 
     86  (\np[=0..2]{nn_fwb}{nn\_fwb}), 
    8587\item 
    8688  the transformation of the solar radiation (if provided as daily mean) into an analytical diurnal cycle 
    87   (\np{ln_dm2dc}{ln\_dm2dc}\forcode{=.true.}), 
    88 \item 
    89   the activation of wave effects from an external wave model  (\np{ln_wave}{ln\_wave}\forcode{=.true.}), 
    90 \item 
    91   a neutral drag coefficient is read from an external wave model (\np{ln_cdgw}{ln\_cdgw}\forcode{=.true.}), 
    92 \item 
    93   the Stokes drift from an external wave model is accounted for (\np{ln_sdw}{ln\_sdw}\forcode{=.true.}), 
    94 \item 
    95   the choice of the Stokes drift profile parameterization (\np{nn_sdrift}{nn\_sdrift}\forcode{=0..2}), 
    96 \item 
    97   the surface stress given to the ocean is modified by surface waves (\np{ln_tauwoc}{ln\_tauwoc}\forcode{=.true.}), 
    98 \item 
    99   the surface stress given to the ocean is read from an external wave model (\np{ln_tauw}{ln\_tauw}\forcode{=.true.}), 
    100 \item 
    101   the Stokes-Coriolis term is included (\np{ln_stcor}{ln\_stcor}\forcode{=.true.}), 
    102 \item 
    103   the light penetration in the ocean (\np{ln_traqsr}{ln\_traqsr}\forcode{=.true.} with namelist \nam{tra_qsr}{tra\_qsr}), 
    104 \item 
    105   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}), 
    106 \item 
    107   the effect of sea-ice pressure on the ocean (\np{ln_ice_embd}{ln\_ice\_embd}\forcode{=.true.}). 
     89  (\np[=.true.]{ln_dm2dc}{ln\_dm2dc}), 
     90\item 
     91  the activation of wave effects from an external wave model  (\np[=.true.]{ln_wave}{ln\_wave}), 
     92\item 
     93  a neutral drag coefficient is read from an external wave model (\np[=.true.]{ln_cdgw}{ln\_cdgw}), 
     94\item 
     95  the Stokes drift from an external wave model is accounted for (\np[=.true.]{ln_sdw}{ln\_sdw}), 
     96\item 
     97  the choice of the Stokes drift profile parameterization (\np[=0..2]{nn_sdrift}{nn\_sdrift}), 
     98\item 
     99  the surface stress given to the ocean is modified by surface waves (\np[=.true.]{ln_tauwoc}{ln\_tauwoc}), 
     100\item 
     101  the surface stress given to the ocean is read from an external wave model (\np[=.true.]{ln_tauw}{ln\_tauw}), 
     102\item 
     103  the Stokes-Coriolis term is included (\np[=.true.]{ln_stcor}{ln\_stcor}), 
     104\item 
     105  the light penetration in the ocean (\np[=.true.]{ln_traqsr}{ln\_traqsr} with namelist \nam{tra_qsr}{tra\_qsr}), 
     106\item 
     107  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}), 
     108\item 
     109  the effect of sea-ice pressure on the ocean (\np[=.true.]{ln_ice_embd}{ln\_ice\_embd}). 
    108110\end{itemize} 
    109111 
     
    142144The latter is the penetrative part of the heat flux. 
    143145It is applied as a 3D trend of the temperature equation (\mdl{traqsr} module) when 
    144 \np{ln_traqsr}{ln\_traqsr}\forcode{=.true.}. 
     146\np[=.true.]{ln_traqsr}{ln\_traqsr}. 
    145147The way the light penetrates inside the water column is generally a sum of decreasing exponentials 
    146148(see \autoref{subsec:TRA_qsr}). 
     
    278280                                  &  daily or weekLL     &  monthly           &  yearly        \\ 
    279281      \hline 
    280       \np{clim}{clim}\forcode{=.false.} &  fn\_yYYYYmMMdDD.nc  &  fn\_yYYYYmMM.nc   &  fn\_yYYYY.nc  \\ 
     282      \np[=.false.]{clim}{clim} &  fn\_yYYYYmMMdDD.nc  &  fn\_yYYYYmMM.nc   &  fn\_yYYYY.nc  \\ 
    281283      \hline 
    282       \np{clim}{clim}\forcode{=.true.}  &  not possible        &  fn\_m??.nc        &  fn            \\ 
     284      \np[=.true.]{clim}{clim}  &  not possible        &  fn\_m??.nc        &  fn            \\ 
    283285      \hline 
    284286    \end{tabular} 
     
    351353However, for forcing data related to the surface module, 
    352354values are not needed at every time-step but at every \np{nn_fsbc}{nn\_fsbc} time-step. 
    353 For example with \np{nn_fsbc}{nn\_fsbc}\forcode{=3}, the surface module will be called at time-steps 1, 4, 7, etc. 
     355For example with \np[=3]{nn_fsbc}{nn\_fsbc}, the surface module will be called at time-steps 1, 4, 7, etc. 
    354356The date used for the time interpolation is thus redefined to the middle of \np{nn_fsbc}{nn\_fsbc} time-step period. 
    355357In the previous example, this leads to: 1h30'00", 4h30'00", 7h30'00", etc. \\ 
     
    550552  Spinup of the iceberg floats 
    551553\item 
    552   Ocean/sea-ice simulation with both models running in parallel (\np{ln_mixcpl}{ln\_mixcpl}\forcode{=.true.}) 
     554  Ocean/sea-ice simulation with both models running in parallel (\np[=.true.]{ln_mixcpl}{ln\_mixcpl}) 
    553555\end{itemize} 
    554556 
     
    605607 
    606608The 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 
    607  (\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. 
     609 (\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. 
    608610 
    609611 
     
    623625%------------------------------------------------------------------------------------------------------------- 
    624626 
    625 In the flux formulation (\np{ln_flx}{ln\_flx}\forcode{=.true.}), 
     627In the flux formulation (\np[=.true.]{ln_flx}{ln\_flx}), 
    626628the surface boundary condition fields are directly read from input files. 
    627629The user has to define in the namelist \nam{sbc_flx}{sbc\_flx} the name of the file, 
     
    731733\begin{itemize} 
    732734\item 
    733   NCAR (\np{ln_NCAR}{ln\_NCAR}\forcode{=.true.}): 
     735  NCAR (\np[=.true.]{ln_NCAR}{ln\_NCAR}): 
    734736  The NCAR bulk formulae have been developed by \citet{large.yeager_rpt04}. 
    735737  They have been designed to handle the NCAR forcing, a mixture of NCEP reanalysis and satellite data. 
     
    741743  This is the so-called DRAKKAR Forcing Set (DFS) \citep{brodeau.barnier.ea_OM10}. 
    742744\item 
    743   COARE 3.0 (\np{ln_COARE_3p0}{ln\_COARE\_3p0}\forcode{=.true.}): 
     745  COARE 3.0 (\np[=.true.]{ln_COARE_3p0}{ln\_COARE\_3p0}): 
    744746  See \citet{fairall.bradley.ea_JC03} for more details 
    745747\item 
    746   COARE 3.5 (\np{ln_COARE_3p5}{ln\_COARE\_3p5}\forcode{=.true.}): 
     748  COARE 3.5 (\np[=.true.]{ln_COARE_3p5}{ln\_COARE\_3p5}): 
    747749  See \citet{edson.jampana.ea_JPO13} for more details 
    748750\item 
    749   ECMWF (\np{ln_ECMWF}{ln\_ECMWF}\forcode{=.true.}): 
     751  ECMWF (\np[=.true.]{ln_ECMWF}{ln\_ECMWF}): 
    750752  Based on \href{https://www.ecmwf.int/node/9221}{IFS (Cy31)} implementation and documentation. 
    751753  Surface roughness lengths needed for the Obukhov length are computed following \citet{beljaars_QJRMS95}. 
     
    762764\begin{itemize} 
    763765\item 
    764   Constant value (\np{constant value}{constant\ value}\forcode{ Cd_ice = 1.4e-3 }): 
     766  Constant value (\np[ Cd_ice=1.4e-3 ]{constant value}{constant\ value}): 
    765767  default constant value used for momentum and heat neutral transfer coefficients 
    766768\item 
    767   \citet{lupkes.gryanik.ea_JGR12} (\np{ln_Cd_L12}{ln\_Cd\_L12}\forcode{=.true.}): 
     769  \citet{lupkes.gryanik.ea_JGR12} (\np[=.true.]{ln_Cd_L12}{ln\_Cd\_L12}): 
    768770  This scheme adds a dependency on edges at leads, melt ponds and flows 
    769771  of the constant neutral air-ice drag. After some approximations, 
     
    773775  It is theoretically applicable to all ice conditions (not only MIZ). 
    774776\item 
    775   \citet{lupkes.gryanik_JGR15} (\np{ln_Cd_L15}{ln\_Cd\_L15}\forcode{=.true.}): 
     777  \citet{lupkes.gryanik_JGR15} (\np[=.true.]{ln_Cd_L15}{ln\_Cd\_L15}): 
    776778  Alternative turbulent transfer coefficients formulation between sea-ice 
    777779  and atmosphere with distinct momentum and heat coefficients depending 
     
    842844 
    843845The optional atmospheric pressure can be used to force ocean and ice dynamics 
    844 (\np{ln_apr_dyn}{ln\_apr\_dyn}\forcode{=.true.}, \nam{sbc}{sbc} namelist). 
     846(\np[=.true.]{ln_apr_dyn}{ln\_apr\_dyn}, \nam{sbc}{sbc} namelist). 
    845847The input atmospheric forcing defined via \np{sn_apr}{sn\_apr} structure (\nam{sbc_apr}{sbc\_apr} namelist) 
    846848can be interpolated in time to the model time step, and even in space when the interpolation on-the-fly is used. 
     
    914916computationally too expensive. Here, two options are available: 
    915917$\Pi_{sal}$ generated by an external model can be read in 
    916 (\np{ln_read_load}{ln\_read\_load}\forcode{ =.true.}), or a ``scalar approximation'' can be 
    917 used (\np{ln_scal_load}{ln\_scal\_load}\forcode{ =.true.}). In the latter case 
     918(\np[=.true.]{ln_read_load}{ln\_read\_load}), or a ``scalar approximation'' can be 
     919used (\np[=.true.]{ln_scal_load}{ln\_scal\_load}). In the latter case 
    918920\[ 
    919921  \Pi_{sal} = \beta \eta, 
     
    10761078\begin{description} 
    10771079 
    1078   \item[\np{nn_isf}{nn\_isf}\forcode{=1}]: 
    1079   The ice shelf cavity is represented (\np{ln_isfcav}{ln\_isfcav}\forcode{=.true.} needed). 
     1080  \item[{\np[=1]{nn_isf}{nn\_isf}}]: 
     1081  The ice shelf cavity is represented (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). 
    10801082  The fwf and heat flux are depending of the local water properties. 
    10811083 
     
    10831085 
    10841086   \begin{description} 
    1085    \item[\np{nn_isfblk}{nn\_isfblk}\forcode{=1}]: 
     1087   \item[{\np[=1]{nn_isfblk}{nn\_isfblk}}]: 
    10861088     The melt rate is based on a balance between the upward ocean heat flux and 
    10871089     the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}. 
    1088    \item[\np{nn_isfblk}{nn\_isfblk}\forcode{=2}]: 
     1090   \item[{\np[=2]{nn_isfblk}{nn\_isfblk}}]: 
    10891091     The melt rate and the heat flux are based on a 3 equations formulation 
    10901092     (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation). 
     
    11031105     There are 3 different ways to compute the exchange coeficient: 
    11041106   \begin{description} 
    1105         \item[\np{nn_gammablk}{nn\_gammablk}\forcode{=0}]: 
     1107        \item[{\np[=0]{nn_gammablk}{nn\_gammablk}}]: 
    11061108     The salt and heat exchange coefficients are constant and defined by \np{rn_gammas0}{rn\_gammas0} and \np{rn_gammat0}{rn\_gammat0}. 
    11071109     \begin{gather*} 
     
    11111113     \end{gather*} 
    11121114     This is the recommended formulation for ISOMIP. 
    1113    \item[\np{nn_gammablk}{nn\_gammablk}\forcode{=1}]: 
     1115   \item[{\np[=1]{nn_gammablk}{nn\_gammablk}}]: 
    11141116     The salt and heat exchange coefficients are velocity dependent and defined as 
    11151117     \begin{gather*} 
     
    11191121     where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters). 
    11201122     See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application. 
    1121    \item[\np{nn_gammablk}{nn\_gammablk}\forcode{=2}]: 
     1123   \item[{\np[=2]{nn_gammablk}{nn\_gammablk}}]: 
    11221124     The salt and heat exchange coefficients are velocity and stability dependent and defined as: 
    11231125\[ 
     
    11301132     This formulation has not been extensively tested in \NEMO\ (not recommended). 
    11311133   \end{description} 
    1132   \item[\np{nn_isf}{nn\_isf}\forcode{=2}]: 
     1134  \item[{\np[=2]{nn_isf}{nn\_isf}}]: 
    11331135   The ice shelf cavity is not represented. 
    11341136   The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. 
    11351137   The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) 
    11361138   (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front 
    1137    (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np{nn_isf}{nn\_isf}\forcode{=3}). 
     1139   (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np[=3]{nn_isf}{nn\_isf}). 
    11381140   The effective melting length (\np{sn_Leff_isf}{sn\_Leff\_isf}) is read from a file. 
    1139   \item[\np{nn_isf}{nn\_isf}\forcode{=3}]: 
     1141  \item[{\np[=3]{nn_isf}{nn\_isf}}]: 
    11401142   The ice shelf cavity is not represented. 
    11411143   The fwf (\np{sn_rnfisf}{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between 
     
    11431145   the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}). 
    11441146   The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
    1145   \item[\np{nn_isf}{nn\_isf}\forcode{=4}]: 
    1146    The ice shelf cavity is opened (\np{ln_isfcav}{ln\_isfcav}\forcode{=.true.} needed). 
     1147  \item[{\np[=4]{nn_isf}{nn\_isf}}]: 
     1148   The ice shelf cavity is opened (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). 
    11471149   However, the fwf is not computed but specified from file \np{sn_fwfisf}{sn\_fwfisf}). 
    11481150   The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
    1149    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})\\ 
     1151   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})\\ 
    11501152\end{description} 
    11511153 
    1152 $\bullet$ \np{nn_isf}{nn\_isf}\forcode{=1} and \np{nn_isf}{nn\_isf}\forcode{=2} compute a melt rate based on 
     1154$\bullet$ \np[=1]{nn_isf}{nn\_isf} and \np[=2]{nn_isf}{nn\_isf} compute a melt rate based on 
    11531155the water mass properties, ocean velocities and depth. 
    11541156This flux is thus highly dependent of the model resolution (horizontal and vertical), 
    11551157realism of the water masses onto the shelf ...\\ 
    11561158 
    1157 $\bullet$ \np{nn_isf}{nn\_isf}\forcode{=3} and \np{nn_isf}{nn\_isf}\forcode{=4} read the melt rate from a file. 
     1159$\bullet$ \np[=3]{nn_isf}{nn\_isf} and \np[=4]{nn_isf}{nn\_isf} read the melt rate from a file. 
    11581160You have total control of the fwf forcing. 
    11591161This can be useful if the water masses on the shelf are not realistic or 
     
    12041206\end{description} 
    12051207 
    1206 If \np{ln_iscpl}{ln\_iscpl}\forcode{=.true.}, the isf draft is assume to be different at each restart step with 
     1208If \np[=.true.]{ln_iscpl}{ln\_iscpl}, the isf draft is assume to be different at each restart step with 
    12071209potentially some new wet/dry cells due to the ice sheet dynamics/thermodynamics. 
    12081210The wetting and drying scheme applied on the restart is very simple and described below for the 6 different possible cases: 
     
    12401242 
    12411243In order to remove the trend and keep the conservation level as close to 0 as possible, 
    1242 a simple conservation scheme is available with \np{ln_hsb}{ln\_hsb}\forcode{=.true.}. 
     1244a simple conservation scheme is available with \np[=.true.]{ln_hsb}{ln\_hsb}. 
    12431245The heat/salt/vol. gain/loss is diagnosed, as well as the location. 
    12441246A correction increment is computed and apply each time step during the next \np{rn_fiscpl}{rn\_fiscpl} time steps. 
     
    12701272which is an integer representing how many icebergs of this class are being described as one lagrangian point 
    12711273(this reduces the numerical problem of tracking every single iceberg). 
    1272 They are enabled by setting \np{ln_icebergs}{ln\_icebergs}\forcode{=.true.}. 
     1274They are enabled by setting \np[=.true.]{ln_icebergs}{ln\_icebergs}. 
    12731275 
    12741276Two initialisation schemes are possible. 
    12751277\begin{description} 
    1276 \item[\np{nn_test_icebergs}{nn\_test\_icebergs}~$>$~0] 
     1278\item[{\np{nn_test_icebergs}{nn\_test\_icebergs}~$>$~0}] 
    12771279  In this scheme, the value of \np{nn_test_icebergs}{nn\_test\_icebergs} represents the class of iceberg to generate 
    12781280  (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 
     
    12811283  \np{nn_test_icebergs}{nn\_test\_icebergs} is defined by four numbers in \np{nn_test_box}{nn\_test\_box} representing the corners of 
    12821284  the geographical box: lonmin,lonmax,latmin,latmax 
    1283 \item[\np{nn_test_icebergs}{nn\_test\_icebergs}\forcode{=-1}] 
     1285\item[{\np[=-1]{nn_test_icebergs}{nn\_test\_icebergs}}] 
    12841286  In this scheme, the model reads a calving file supplied in the \np{sn_icb}{sn\_icb} parameter. 
    12851287  This should be a file with a field on the configuration grid (typically ORCA) 
     
    13061308The amount of information is controlled by two integer parameters: 
    13071309\begin{description} 
    1308 \item[\np{nn_verbose_level}{nn\_verbose\_level}] takes a value between one and four and 
     1310\item[{\np{nn_verbose_level}{nn\_verbose\_level}}] takes a value between one and four and 
    13091311  represents an increasing number of points in the code at which variables are written, 
    13101312  and an increasing level of obscurity. 
    1311 \item[\np{nn_verbose_write}{nn\_verbose\_write}] is the number of timesteps between writes 
     1313\item[{\np{nn_verbose_write}{nn\_verbose\_write}}] is the number of timesteps between writes 
    13121314\end{description} 
    13131315 
     
    13431345 
    13441346Physical processes related to ocean surface waves can be accounted by setting the logical variable 
    1345 \np{ln_wave}{ln\_wave}\forcode{=.true.} in \nam{sbc}{sbc} namelist. In addition, specific flags accounting for 
     1347\np[=.true.]{ln_wave}{ln\_wave} in \nam{sbc}{sbc} namelist. In addition, specific flags accounting for 
    13461348different processes should be activated as explained in the following sections. 
    13471349 
     
    13511353for external data names, locations, frequency, interpolation and all the miscellanous options allowed by 
    13521354Input Data generic Interface (see \autoref{sec:SBC_input}). 
    1353 \item[coupled mode]: \NEMO\ and an external wave model can be coupled by setting \np{ln_cpl}{ln\_cpl} \forcode{= .true.} 
     1355\item[coupled mode]: \NEMO\ and an external wave model can be coupled by setting \np[=.true.]{ln_cpl}{ln\_cpl} 
    13541356in \nam{sbc}{sbc} namelist and filling the \nam{sbc_cpl}{sbc\_cpl} namelist. 
    13551357\end{description} 
     
    13641366 
    13651367The neutral surface drag coefficient provided from an external data source (\ie\ a wave model), 
    1366 can be used by setting the logical variable \np{ln_cdgw}{ln\_cdgw} \forcode{= .true.} in \nam{sbc}{sbc} namelist. 
     1368can be used by setting the logical variable \np[=.true.]{ln_cdgw}{ln\_cdgw} in \nam{sbc}{sbc} namelist. 
    13671369Then using the routine \rou{sbcblk\_algo\_ncar} and starting from the neutral drag coefficent provided, 
    13681370the drag coefficient is computed according to the stable/unstable conditions of the 
     
    14081410 
    14091411\begin{description} 
    1410 \item[\np{nn_sdrift}{nn\_sdrift} = 0]: exponential integral profile parameterization proposed by 
     1412\item[{\np{nn_sdrift}{nn\_sdrift} = 0}]: exponential integral profile parameterization proposed by 
    14111413\citet{breivik.janssen.ea_JPO14}: 
    14121414 
     
    14271429where $H_s$ is the significant wave height and $\omega$ is the wave frequency. 
    14281430 
    1429 \item[\np{nn_sdrift}{nn\_sdrift} = 1]: velocity profile based on the Phillips spectrum which is considered to be a 
     1431\item[{\np{nn_sdrift}{nn\_sdrift} = 1}]: velocity profile based on the Phillips spectrum which is considered to be a 
    14301432reasonable estimate of the part of the spectrum mostly contributing to the Stokes drift velocity near the surface 
    14311433\citep{breivik.bidlot.ea_OM16}: 
     
    14391441where $erf$ is the complementary error function and $k_p$ is the peak wavenumber. 
    14401442 
    1441 \item[\np{nn_sdrift}{nn\_sdrift} = 2]: velocity profile based on the Phillips spectrum as for \np{nn_sdrift}{nn\_sdrift} = 1 
     1443\item[{\np{nn_sdrift}{nn\_sdrift} = 2}]: velocity profile based on the Phillips spectrum as for \np{nn_sdrift}{nn\_sdrift} = 1 
    14421444but using the wave frequency from a wave model. 
    14431445 
     
    14771479In order to include this term, once evaluated the Stokes drift (using one of the 3 possible 
    14781480approximations described in \autoref{subsec:SBC_wave_sdw}), 
    1479 \np{ln_stcor}{ln\_stcor}\forcode{=.true.} has to be set. 
     1481\np[=.true.]{ln_stcor}{ln\_stcor} has to be set. 
    14801482 
    14811483 
     
    15171519 
    15181520The wave stress derived from an external wave model can be provided either through the normalized 
    1519 wave stress into the ocean by setting \np{ln_tauwoc}{ln\_tauwoc}\forcode{=.true.}, or through the zonal and 
    1520 meridional stress components by setting \np{ln_tauw}{ln\_tauw}\forcode{=.true.}. 
     1521wave stress into the ocean by setting \np[=.true.]{ln_tauwoc}{ln\_tauwoc}, or through the zonal and 
     1522meridional stress components by setting \np[=.true.]{ln_tauw}{ln\_tauw}. 
    15211523 
    15221524 
     
    15611563assuming that the diurnal cycle of SWF is a scaling of the top of the atmosphere diurnal cycle of incident SWF. 
    15621564The \cite{bernie.guilyardi.ea_CD07} reconstruction algorithm is available in \NEMO\ by 
    1563 setting \np{ln_dm2dc}{ln\_dm2dc}\forcode{=.true.} (a \textit{\nam{sbc}{sbc}} namelist variable) when 
    1564 using a bulk formulation (\np{ln_blk}{ln\_blk}\forcode{=.true.}) or 
    1565 the flux formulation (\np{ln_flx}{ln\_flx}\forcode{=.true.}). 
     1565setting \np[=.true.]{ln_dm2dc}{ln\_dm2dc} (a \textit{\nam{sbc}{sbc}} namelist variable) when 
     1566using a bulk formulation (\np[=.true.]{ln_blk}{ln\_blk}) or 
     1567the flux formulation (\np[=.true.]{ln_flx}{ln\_flx}). 
    15661568The reconstruction is performed in the \mdl{sbcdcy} module. 
    15671569The detail of the algoritm used can be found in the appendix~A of \cite{bernie.guilyardi.ea_CD07}. 
     
    15981600\label{subsec:SBC_rotation} 
    15991601 
    1600 When using a flux (\np{ln_flx}{ln\_flx}\forcode{=.true.}) or bulk (\np{ln_blk}{ln\_blk}\forcode{=.true.}) formulation, 
     1602When using a flux (\np[=.true.]{ln_flx}{ln\_flx}) or bulk (\np[=.true.]{ln_blk}{ln\_blk}) formulation, 
    16011603pairs of vector components can be rotated from east-north directions onto the local grid directions. 
    16021604This is particularly useful when interpolation on the fly is used since here any vectors are likely to 
     
    16271629 
    16281630Options are defined through the \nam{sbc_ssr}{sbc\_ssr} namelist variables. 
    1629 On forced mode using a flux formulation (\np{ln_flx}{ln\_flx}\forcode{=.true.}), 
     1631On forced mode using a flux formulation (\np[=.true.]{ln_flx}{ln\_flx}), 
    16301632a feedback term \emph{must} be added to the surface heat flux $Q_{ns}^o$: 
    16311633\[ 
     
    17461748 
    17471749\begin{description} 
    1748 \item[\np{nn_fwb}{nn\_fwb}\forcode{=0}] 
     1750\item[{\np[=0]{nn_fwb}{nn\_fwb}}] 
    17491751  no control at all. 
    17501752  The mean sea level is free to drift, and will certainly do so. 
    1751 \item[\np{nn_fwb}{nn\_fwb}\forcode{=1}] 
     1753\item[{\np[=1]{nn_fwb}{nn\_fwb}}] 
    17521754  global mean \textit{emp} set to zero at each model time step. 
    17531755  %GS: comment below still relevant ? 
    17541756  %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). 
    1755 \item[\np{nn_fwb}{nn\_fwb}\forcode{=2}] 
     1757\item[{\np[=2]{nn_fwb}{nn\_fwb}}] 
    17561758  freshwater budget is adjusted from the previous year annual mean budget which 
    17571759  is read in the \textit{EMPave\_old.dat} file. 
     
    17831785 
    17841786 
    1785 \biblio 
    1786  
    1787 \pindex 
     1787\onlyinsubfile{\bibliography{../main/bibliography}} 
     1788 
     1789\onlyinsubfile{\printindex} 
    17881790 
    17891791\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_STO.tex

    r11578 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    186188 
    187189\begin{description} 
    188 \item[\np{nn_sto_eos}{nn\_sto\_eos}:]   number of independent random walks 
    189 \item[\np{rn_eos_stdxy}{rn\_eos\_stdxy}:] random walk horizontal standard deviation (in grid points) 
    190 \item[\np{rn_eos_stdz}{rn\_eos\_stdz}:]  random walk vertical standard deviation (in grid points) 
    191 \item[\np{rn_eos_tcor}{rn\_eos\_tcor}:]  random walk time correlation (in timesteps) 
    192 \item[\np{nn_eos_ord}{nn\_eos\_ord}:]   order of autoregressive processes 
    193 \item[\np{nn_eos_flt}{nn\_eos\_flt}:]   passes of Laplacian filter 
    194 \item[\np{rn_eos_lim}{rn\_eos\_lim}:]   limitation factor (default = 3.0) 
     190\item[{\np{nn_sto_eos}{nn\_sto\_eos}:}]   number of independent random walks 
     191\item[{\np{rn_eos_stdxy}{rn\_eos\_stdxy}:}] random walk horizontal standard deviation (in grid points) 
     192\item[{\np{rn_eos_stdz}{rn\_eos\_stdz}:}]  random walk vertical standard deviation (in grid points) 
     193\item[{\np{rn_eos_tcor}{rn\_eos\_tcor}:}]  random walk time correlation (in timesteps) 
     194\item[{\np{nn_eos_ord}{nn\_eos\_ord}:}]   order of autoregressive processes 
     195\item[{\np{nn_eos_flt}{nn\_eos\_flt}:}]   passes of Laplacian filter 
     196\item[{\np{rn_eos_lim}{rn\_eos\_lim}:}]   limitation factor (default = 3.0) 
    195197\end{description} 
    196198 
    197199The first four parameters define the stochastic part of equation of state. 
    198 \biblio 
    199  
    200 \pindex 
     200\onlyinsubfile{\bibliography{../main/bibliography}} 
     201 
     202\onlyinsubfile{\printindex} 
    201203 
    202204\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex

    r11578 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    5557 
    5658The user has the option of extracting each tendency term on the RHS of the tracer equation for output 
    57 (\np{ln_tra_trd}{ln\_tra\_trd} or \np{ln_tra_mxl}{ln\_tra\_mxl}\forcode{=.true.}), as described in \autoref{chap:DIA}. 
     59(\np{ln_tra_trd}{ln\_tra\_trd} or \np[=.true.]{ln_tra_mxl}{ln\_tra\_mxl}), as described in \autoref{chap:DIA}. 
    5860 
    5961% ================================================================ 
     
    8587Indeed, it is obtained by using the following equality: $\nabla \cdot (\vect U \, T) = \vect U \cdot \nabla T$ which 
    8688results from the use of the continuity equation, $\partial_t e_3 + e_3 \; \nabla \cdot \vect U = 0$ 
    87 (which reduces to $\nabla \cdot \vect U = 0$ in linear free surface, \ie\ \np{ln_linssh}{ln\_linssh}\forcode{=.true.}). 
     89(which reduces to $\nabla \cdot \vect U = 0$ in linear free surface, \ie\ \np[=.true.]{ln_linssh}{ln\_linssh}). 
    8890Therefore it is of paramount importance to design the discrete analogue of the advection tendency so that 
    8991it is consistent with the continuity equation in order to enforce the conservation properties of 
     
    121123\begin{description} 
    122124\item[linear free surface:] 
    123   (\np{ln_linssh}{ln\_linssh}\forcode{=.true.}) 
     125  (\np[=.true.]{ln_linssh}{ln\_linssh}) 
    124126  the first level thickness is constant in time: 
    125127  the vertical boundary condition is applied at the fixed surface $z = 0$ rather than on 
     
    129131  the first level tracer value. 
    130132\item[non-linear free surface:] 
    131   (\np{ln_linssh}{ln\_linssh}\forcode{=.false.}) 
     133  (\np[=.false.]{ln_linssh}{ln\_linssh}) 
    132134  convergence/divergence in the first ocean level moves the free surface up/down. 
    133135  There is no tracer advection through it so that the advective fluxes through the surface are also zero. 
     
    190192%        2nd order centred scheme 
    191193 
    192 The centred advection scheme (CEN) is used when \np{ln_traadv_cen}{ln\_traadv\_cen}\forcode{=.true.}. 
     194The centred advection scheme (CEN) is used when \np[=.true.]{ln_traadv_cen}{ln\_traadv\_cen}. 
    193195Its order ($2^{nd}$ or $4^{th}$) can be chosen independently on horizontal (iso-level) and vertical direction by 
    194196setting \np{nn_cen_h}{nn\_cen\_h} and \np{nn_cen_v}{nn\_cen\_v} to $2$ or $4$. 
     
    222224  \tau_u^{cen4} = \overline{T - \frac{1}{6} \, \delta_i \Big[ \delta_{i + 1/2}[T] \, \Big]}^{\,i + 1/2} 
    223225\end{equation} 
    224 In the vertical direction (\np{nn_cen_v}{nn\_cen\_v}\forcode{=4}), 
     226In the vertical direction (\np[=4]{nn_cen_v}{nn\_cen\_v}), 
    225227a $4^{th}$ COMPACT interpolation has been prefered \citep{demange_phd14}. 
    226228In the COMPACT scheme, both the field and its derivative are interpolated, which leads, after a matrix inversion, 
     
    255257\label{subsec:TRA_adv_tvd} 
    256258 
    257 The Flux Corrected Transport schemes (FCT) is used when \np{ln_traadv_fct}{ln\_traadv\_fct}\forcode{=.true.}. 
     259The Flux Corrected Transport schemes (FCT) is used when \np[=.true.]{ln_traadv_fct}{ln\_traadv\_fct}. 
    258260Its order ($2^{nd}$ or $4^{th}$) can be chosen independently on horizontal (iso-level) and vertical direction by 
    259261setting \np{nn_fct_h}{nn\_fct\_h} and \np{nn_fct_v}{nn\_fct\_v} to $2$ or $4$. 
     
    298300\label{subsec:TRA_adv_mus} 
    299301 
    300 The Monotone Upstream Scheme for Conservative Laws (MUSCL) is used when \np{ln_traadv_mus}{ln\_traadv\_mus}\forcode{=.true.}. 
     302The Monotone Upstream Scheme for Conservative Laws (MUSCL) is used when \np[=.true.]{ln_traadv_mus}{ln\_traadv\_mus}. 
    301303MUSCL implementation can be found in the \mdl{traadv\_mus} module. 
    302304 
     
    326328This choice ensure the \textit{positive} character of the scheme. 
    327329In addition, fluxes round a grid-point where a runoff is applied can optionally be computed using upstream fluxes 
    328 (\np{ln_mus_ups}{ln\_mus\_ups}\forcode{=.true.}). 
     330(\np[=.true.]{ln_mus_ups}{ln\_mus\_ups}). 
    329331 
    330332% ------------------------------------------------------------------------------------------------------------- 
     
    334336\label{subsec:TRA_adv_ubs} 
    335337 
    336 The Upstream-Biased Scheme (UBS) is used when \np{ln_traadv_ubs}{ln\_traadv\_ubs}\forcode{=.true.}. 
     338The Upstream-Biased Scheme (UBS) is used when \np[=.true.]{ln_traadv_ubs}{ln\_traadv\_ubs}. 
    337339UBS implementation can be found in the \mdl{traadv\_mus} module. 
    338340 
     
    364366\citep{shchepetkin.mcwilliams_OM05, demange_phd14}. 
    365367Therefore the vertical flux is evaluated using either a $2^nd$ order FCT scheme or a $4^th$ order COMPACT scheme 
    366 (\np{nn_ubs_v}{nn\_ubs\_v}\forcode{=2 or 4}). 
     368(\np[=2 or 4]{nn_ubs_v}{nn\_ubs\_v}). 
    367369 
    368370For stability reasons (see \autoref{chap:TD}), the first term  in \autoref{eq:TRA_adv_ubs} 
     
    407409 
    408410The Quadratic Upstream Interpolation for Convective Kinematics with Estimated Streaming Terms (QUICKEST) scheme 
    409 proposed by \citet{leonard_CMAME79} is used when \np{ln_traadv_qck}{ln\_traadv\_qck}\forcode{=.true.}. 
     411proposed by \citet{leonard_CMAME79} is used when \np[=.true.]{ln_traadv_qck}{ln\_traadv\_qck}. 
    410412QUICKEST implementation can be found in the \mdl{traadv\_qck} module. 
    411413 
     
    452454except for the pure vertical component that appears when a rotation tensor is used. 
    453455This latter component is solved implicitly together with the vertical diffusion term (see \autoref{chap:TD}). 
    454 When \np{ln_traldf_msc}{ln\_traldf\_msc}\forcode{=.true.}, a Method of Stabilizing Correction is used in which 
     456When \np[=.true.]{ln_traldf_msc}{ln\_traldf\_msc}, a Method of Stabilizing Correction is used in which 
    455457the pure vertical component is split into an explicit and an implicit part \citep{lemarie.debreu.ea_OM12}. 
    456458 
     
    464466 
    465467\begin{description} 
    466 \item[\np{ln_traldf_OFF}{ln\_traldf\_OFF}\forcode{=.true.}:] 
     468\item[{\np[=.true.]{ln_traldf_OFF}{ln\_traldf\_OFF}}] 
    467469  no operator selected, the lateral diffusive tendency will not be applied to the tracer equation. 
    468470  This option can be used when the selected advection scheme is diffusive enough (MUSCL scheme for example). 
    469 \item[\np{ln_traldf_lap}{ln\_traldf\_lap}\forcode{=.true.}:] 
     471\item[{\np[=.true.]{ln_traldf_lap}{ln\_traldf\_lap}}] 
    470472  a laplacian operator is selected. 
    471473  This harmonic operator takes the following expression:  $\mathcal{L}(T) = \nabla \cdot A_{ht} \; \nabla T $, 
    472474  where the gradient operates along the selected direction (see \autoref{subsec:TRA_ldf_dir}), 
    473475  and $A_{ht}$ is the eddy diffusivity coefficient expressed in $m^2/s$ (see \autoref{chap:LDF}). 
    474 \item[\np{ln_traldf_blp}{ln\_traldf\_blp}\forcode{=.true.}]: 
     476\item[{\np[=.true.]{ln_traldf_blp}{ln\_traldf\_blp}}]: 
    475477  a bilaplacian operator is selected. 
    476478  This biharmonic operator takes the following expression: 
     
    497499The choice of a direction of action determines the form of operator used. 
    498500The operator is a simple (re-entrant) laplacian acting in the (\textbf{i},\textbf{j}) plane when 
    499 iso-level option is used (\np{ln_traldf_lev}{ln\_traldf\_lev}\forcode{=.true.}) or 
     501iso-level option is used (\np[=.true.]{ln_traldf_lev}{ln\_traldf\_lev}) or 
    500502when a horizontal (\ie\ geopotential) operator is demanded in \textit{z}-coordinate 
    501 (\np{ln_traldf_hor}{ln\_traldf\_hor} and \np{ln_zco}{ln\_zco}\forcode{=.true.}). 
     503(\np{ln_traldf_hor}{ln\_traldf\_hor} and \np[=.true.]{ln_zco}{ln\_zco}). 
    502504The associated code can be found in the \mdl{traldf\_lap\_blp} module. 
    503505The operator is a rotated (re-entrant) laplacian when 
     
    536538It is a \textit{horizontal} operator (\ie acting along geopotential surfaces) in 
    537539the $z$-coordinate with or without partial steps, but is simply an iso-level operator in the $s$-coordinate. 
    538 It is thus used when, in addition to \np{ln_traldf_lap}{ln\_traldf\_lap} or \np{ln_traldf_blp}{ln\_traldf\_blp}\forcode{=.true.}, 
    539 we have \np{ln_traldf_lev}{ln\_traldf\_lev}\forcode{=.true.} or \np{ln_traldf_hor}{ln\_traldf\_hor}~=~\np{ln_zco}{ln\_zco}\forcode{=.true.}. 
     540It is thus used when, in addition to \np{ln_traldf_lap}{ln\_traldf\_lap} or \np[=.true.]{ln_traldf_blp}{ln\_traldf\_blp}, 
     541we have \np[=.true.]{ln_traldf_lev}{ln\_traldf\_lev} or \np{ln_traldf_hor}{ln\_traldf\_hor}~=~\np[=.true.]{ln_zco}{ln\_zco}. 
    540542In both cases, it significantly contributes to diapycnal mixing. 
    541543It is therefore never recommended, even when using it in the bilaplacian case. 
    542544 
    543 Note that in the partial step $z$-coordinate (\np{ln_zps}{ln\_zps}\forcode{=.true.}), 
     545Note that in the partial step $z$-coordinate (\np[=.true.]{ln_zps}{ln\_zps}), 
    544546tracers in horizontally adjacent cells are located at different depths in the vicinity of the bottom. 
    545547In this case, horizontal derivatives in (\autoref{eq:TRA_ldf_lap}) at the bottom level require a specific treatment. 
     
    573575$r_1$ and $r_2$ are the slopes between the surface of computation ($z$- or $s$-surfaces) and 
    574576the surface along which the diffusion operator acts (\ie\ horizontal or iso-neutral surfaces). 
    575 It is thus used when, in addition to \np{ln_traldf_lap}{ln\_traldf\_lap}\forcode{=.true.}, 
    576 we have \np{ln_traldf_iso}{ln\_traldf\_iso}\forcode{=.true.}, 
    577 or both \np{ln_traldf_hor}{ln\_traldf\_hor}\forcode{=.true.} and \np{ln_zco}{ln\_zco}\forcode{=.true.}. 
     577It is thus used when, in addition to \np[=.true.]{ln_traldf_lap}{ln\_traldf\_lap}, 
     578we have \np[=.true.]{ln_traldf_iso}{ln\_traldf\_iso}, 
     579or both \np[=.true.]{ln_traldf_hor}{ln\_traldf\_hor} and \np[=.true.]{ln_zco}{ln\_zco}. 
    578580The way these slopes are evaluated is given in \autoref{sec:LDF_slp}. 
    579581At the surface, bottom and lateral boundaries, the turbulent fluxes of heat and salt are set to zero using 
     
    591593any additional background horizontal diffusion \citep{guilyardi.madec.ea_CD01}. 
    592594 
    593 Note that in the partial step $z$-coordinate (\np{ln_zps}{ln\_zps}\forcode{=.true.}), 
     595Note that in the partial step $z$-coordinate (\np[=.true.]{ln_zps}{ln\_zps}), 
    594596the horizontal derivatives at the bottom level in \autoref{eq:TRA_ldf_iso} require a specific treatment. 
    595597They are calculated in module zpshde, described in \autoref{sec:TRA_zpshde}. 
     
    601603 
    602604An alternative scheme developed by \cite{griffies.gnanadesikan.ea_JPO98} which ensures tracer variance decreases 
    603 is also available in \NEMO\ (\np{ln_traldf_triad}{ln\_traldf\_triad}\forcode{=.true.}). 
     605is also available in \NEMO\ (\np[=.true.]{ln_traldf_triad}{ln\_traldf\_triad}). 
    604606A complete description of the algorithm is given in \autoref{apdx:TRIADS}. 
    605607 
     
    647649respectively. 
    648650Generally, $A_w^{vT} = A_w^{vS}$ except when double diffusive mixing is parameterised 
    649 (\ie\ \np{ln_zdfddm}{ln\_zdfddm}\forcode{=.true.},). 
     651(\ie\ \np[=.true.]{ln_zdfddm}{ln\_zdfddm},). 
    650652The way these coefficients are evaluated is given in \autoref{chap:ZDF} (ZDF). 
    651653Furthermore, when iso-neutral mixing is used, both mixing coefficients are increased by 
     
    722724Such time averaging prevents the divergence of odd and even time step (see \autoref{chap:TD}). 
    723725 
    724 In the linear free surface case (\np{ln_linssh}{ln\_linssh}\forcode{=.true.}), an additional term has to be added on 
     726In the linear free surface case (\np[=.true.]{ln_linssh}{ln\_linssh}), an additional term has to be added on 
    725727both temperature and salinity. 
    726728On temperature, this term remove the heat content associated with mass exchange that has been added to $Q_{ns}$. 
     
    757759 
    758760Options are defined through the \nam{tra_qsr}{tra\_qsr} namelist variables. 
    759 When the penetrative solar radiation option is used (\np{ln_traqsr}{ln\_traqsr}\forcode{=.true.}), 
     761When the penetrative solar radiation option is used (\np[=.true.]{ln_traqsr}{ln\_traqsr}), 
    760762the solar radiation penetrates the top few tens of meters of the ocean. 
    761 If it is not used (\np{ln_traqsr}{ln\_traqsr}\forcode{=.false.}) all the heat flux is absorbed in the first ocean level. 
     763If it is not used (\np[=.false.]{ln_traqsr}{ln\_traqsr}) all the heat flux is absorbed in the first ocean level. 
    762764Thus, in the former case a term is added to the time evolution equation of temperature \autoref{eq:MB_PE_tra_T} and 
    763765the surface boundary condition is modified to take into account only the non-penetrative part of the surface 
     
    788790larger depths where it contributes to local heating. 
    789791The way this second part of the solar energy penetrates into the ocean depends on which formulation is chosen. 
    790 In the simple 2-waveband light penetration scheme (\np{ln_qsr_2bd}{ln\_qsr\_2bd}\forcode{=.true.}) 
     792In the simple 2-waveband light penetration scheme (\np[=.true.]{ln_qsr_2bd}{ln\_qsr\_2bd}) 
    791793a chlorophyll-independent monochromatic formulation is chosen for the shorter wavelengths, 
    792794leading to the following expression \citep{paulson.simpson_JPO77}: 
     
    816818The 2-bands formulation does not reproduce the full model very well. 
    817819 
    818 The RGB formulation is used when \np{ln_qsr_rgb}{ln\_qsr\_rgb}\forcode{=.true.}. 
     820The RGB formulation is used when \np[=.true.]{ln_qsr_rgb}{ln\_qsr\_rgb}. 
    819821The RGB attenuation coefficients (\ie\ the inverses of the extinction length scales) are tabulated over 
    82082261 nonuniform chlorophyll classes ranging from 0.01 to 10 g.Chl/L 
     
    823825 
    824826\begin{description} 
    825 \item[\np{nn_chldta}{nn\_chldta}\forcode{=0}] 
     827\item[{\np[=0]{nn_chldta}{nn\_chldta}}] 
    826828  a constant 0.05 g.Chl/L value everywhere ; 
    827 \item[\np{nn_chldta}{nn\_chldta}\forcode{=1}] 
     829\item[{\np[=1]{nn_chldta}{nn\_chldta}}] 
    828830  an observed time varying chlorophyll deduced from satellite surface ocean color measurement spread uniformly in 
    829831  the vertical direction; 
    830 \item[\np{nn_chldta}{nn\_chldta}\forcode{=2}] 
     832\item[{\np[=2]{nn_chldta}{nn\_chldta}}] 
    831833  same as previous case except that a vertical profile of chlorophyl is used. 
    832834  Following \cite{morel.berthon_LO89}, the profile is computed from the local surface chlorophyll value; 
    833 \item[\np{ln_qsr_bio}{ln\_qsr\_bio}\forcode{=.true.}] 
     835\item[{\np[=.true.]{ln_qsr_bio}{ln\_qsr\_bio}}] 
    834836  simulated time varying chlorophyll by TOP biogeochemical model. 
    835837  In this case, the RGB formulation is used to calculate both the phytoplankton light limitation in 
     
    944946%        Diffusive BBL 
    945947% ------------------------------------------------------------------------------------------------------------- 
    946 \subsection[Diffusive bottom boundary layer (\forcode{nn_bbl_ldf=1})]{Diffusive bottom boundary layer (\protect\np{nn_bbl_ldf}{nn\_bbl\_ldf}\forcode{=1})} 
     948\subsection[Diffusive bottom boundary layer (\forcode{nn_bbl_ldf=1})]{Diffusive bottom boundary layer (\protect\np[=1]{nn_bbl_ldf}{nn\_bbl\_ldf})} 
    947949\label{subsec:TRA_bbl_diff} 
    948950 
    949 When applying sigma-diffusion (\np{ln_trabbl}{ln\_trabbl}\forcode{=.true.} and \np{nn_bbl_ldf}{nn\_bbl\_ldf} set to 1), 
     951When applying sigma-diffusion (\np[=.true.]{ln_trabbl}{ln\_trabbl} and \np{nn_bbl_ldf}{nn\_bbl\_ldf} set to 1), 
    950952the diffusive flux between two adjacent cells at the ocean floor is given by 
    951953\[ 
     
    983985%        Advective BBL 
    984986% ------------------------------------------------------------------------------------------------------------- 
    985 \subsection[Advective bottom boundary layer (\forcode{nn_bbl_adv=1,2})]{Advective bottom boundary layer (\protect\np{nn_bbl_adv}{nn\_bbl\_adv}\forcode{=1,2})} 
     987\subsection[Advective bottom boundary layer (\forcode{nn_bbl_adv=1,2})]{Advective bottom boundary layer (\protect\np[=1,2]{nn_bbl_adv}{nn\_bbl\_adv})} 
    986988\label{subsec:TRA_bbl_adv} 
    987989 
     
    10141016%%%gmcomment   :  this section has to be really written 
    10151017 
    1016 When applying an advective BBL (\np{nn_bbl_adv}{nn\_bbl\_adv}\forcode{=1..2}), an overturning circulation is added which 
     1018When applying an advective BBL (\np[=1..2]{nn_bbl_adv}{nn\_bbl\_adv}), an overturning circulation is added which 
    10171019connects two adjacent bottom grid-points only if dense water overlies less dense water on the slope. 
    10181020The density difference causes dense water to move down the slope. 
    10191021 
    1020 \np{nn_bbl_adv}{nn\_bbl\_adv}\forcode{=1}: 
     1022\np[=1]{nn_bbl_adv}{nn\_bbl\_adv}: 
    10211023the downslope velocity is chosen to be the Eulerian ocean velocity just above the topographic step 
    10221024(see black arrow in \autoref{fig:TRA_bbl}) \citep{beckmann.doscher_JPO97}. 
     
    10251027if the velocity is directed towards greater depth (\ie\ $\vect U \cdot \nabla H > 0$). 
    10261028 
    1027 \np{nn_bbl_adv}{nn\_bbl\_adv}\forcode{=2}: 
     1029\np[=2]{nn_bbl_adv}{nn\_bbl\_adv}: 
    10281030the downslope velocity is chosen to be proportional to $\Delta \rho$, 
    10291031the density difference between the higher cell and lower cell densities \citep{campin.goosse_T99}. 
     
    11531155(\ie\ fluxes plus content in mass exchanges). 
    11541156$\gamma$ is initialized as \np{rn_atfp}{rn\_atfp} (\textbf{namelist} parameter). 
    1155 Its default value is \np{rn_atfp}{rn\_atfp}\forcode{=10.e-3}. 
     1157Its default value is \np[=10.e-3]{rn_atfp}{rn\_atfp}. 
    11561158Note that the forcing correction term in the filter is not applied in linear free surface 
    11571159(\jp{ln\_linssh}\forcode{=.true.}) (see \autoref{subsec:TRA_sbc}). 
     
    12161218 
    12171219\begin{description} 
    1218 \item[\np{ln_teos10}{ln\_teos10}\forcode{=.true.}] 
     1220\item[{\np[=.true.]{ln_teos10}{ln\_teos10}}] 
    12191221  the polyTEOS10-bsq equation of seawater \citep{roquet.madec.ea_OM15} is used. 
    12201222  The accuracy of this approximation is comparable to the TEOS-10 rational function approximation, 
     
    12351237  either computing the air-sea and ice-sea fluxes (forced mode) or 
    12361238  sending the SST field to the atmosphere (coupled mode). 
    1237 \item[\np{ln_eos80}{ln\_eos80}\forcode{=.true.}] 
     1239\item[{\np[=.true.]{ln_eos80}{ln\_eos80}}] 
    12381240  the polyEOS80-bsq equation of seawater is used. 
    12391241  It takes the same polynomial form as the polyTEOS10, but the coefficients have been optimized to 
     
    12471249  Nevertheless, a severe assumption is made in order to have a heat content ($C_p T_p$) which 
    12481250  is conserved by the model: $C_p$ is set to a constant value, the TEOS10 value. 
    1249 \item[\np{ln_seos}{ln\_seos}\forcode{=.true.}] 
     1251\item[{\np[=.true.]{ln_seos}{ln\_seos}}] 
    12501252  a simplified EOS (S-EOS) inspired by \citet{vallis_bk06} is chosen, 
    12511253  the coefficients of which has been optimized to fit the behavior of TEOS10 
     
    13671369I've changed "derivative" to "difference" and "mean" to "average"} 
    13681370 
    1369 With partial cells (\np{ln_zps}{ln\_zps}\forcode{=.true.}) at bottom and top (\np{ln_isfcav}{ln\_isfcav}\forcode{=.true.}), 
     1371With partial cells (\np[=.true.]{ln_zps}{ln\_zps}) at bottom and top (\np[=.true.]{ln_isfcav}{ln\_isfcav}), 
    13701372in general, tracers in horizontally adjacent cells live at different depths. 
    13711373Horizontal gradients of tracers are needed for horizontal diffusion (\mdl{traldf} module) and 
    13721374the hydrostatic pressure gradient calculations (\mdl{dynhpg} module). 
    1373 The partial cell properties at the top (\np{ln_isfcav}{ln\_isfcav}\forcode{=.true.}) are computed in the same way as 
     1375The partial cell properties at the top (\np[=.true.]{ln_isfcav}{ln\_isfcav}) are computed in the same way as 
    13741376for the bottom. 
    13751377So, only the bottom interpolation is explained below. 
     
    13871389  the $z$-partial step coordinate]{ 
    13881390    Discretisation of the horizontal difference and average of tracers in 
    1389     the $z$-partial step coordinate (\protect\np{ln_zps}{ln\_zps}\forcode{=.true.}) in 
     1391    the $z$-partial step coordinate (\protect\np[=.true.]{ln_zps}{ln\_zps}) in 
    13901392    the case $(e3w_k^{i + 1} - e3w_k^i) > 0$. 
    13911393    A linear interpolation is used to estimate $\widetilde T_k^{i + 1}$, 
     
    14591461%%% 
    14601462 
    1461 \biblio 
    1462  
    1463 \pindex 
     1463\onlyinsubfile{\bibliography{../main/bibliography}} 
     1464 
     1465\onlyinsubfile{\printindex} 
    14641466 
    14651467\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex

    r11578 r11582  
    33%% Custom aliases 
    44\newcommand{\cf}{\ensuremath{C\kern-0.14em f}} 
     5 
     6\onlyinsubfile{\makeindex} 
    57 
    68\begin{document} 
     
    4244are computed and added to the general trend in the \mdl{dynzdf} and \mdl{trazdf} modules, respectively. 
    4345%These trends can be computed using either a forward time stepping scheme 
    44 %(namelist parameter \np{ln_zdfexp}{ln\_zdfexp}\forcode{=.true.}) or a backward time stepping scheme 
    45 %(\np{ln_zdfexp}{ln\_zdfexp}\forcode{=.false.}) depending on the magnitude of the mixing coefficients, 
     46%(namelist parameter \np[=.true.]{ln_zdfexp}{ln\_zdfexp}) or a backward time stepping scheme 
     47%(\np[=.false.]{ln_zdfexp}{ln\_zdfexp}) depending on the magnitude of the mixing coefficients, 
    4648%and thus of the formulation used (see \autoref{chap:TD}). 
    4749 
     
    9294%-------------------------------------------------------------------------------------------------------------- 
    9395 
    94 When \np{ln_zdfric}{ln\_zdfric}\forcode{=.true.}, a local Richardson number dependent formulation for the vertical momentum and 
     96When \np[=.true.]{ln_zdfric}{ln\_zdfric}, a local Richardson number dependent formulation for the vertical momentum and 
    9597tracer eddy coefficients is set through the \nam{zdf_ric}{zdf\_ric} namelist variables. 
    9698The vertical mixing coefficients are diagnosed from the large scale variables computed by the model. 
     
    118120 
    119121A simple mixing-layer model to transfer and dissipate the atmospheric forcings 
    120 (wind-stress and buoyancy fluxes) can be activated setting the \np{ln_mldw}{ln\_mldw}\forcode{=.true.} in the namelist. 
     122(wind-stress and buoyancy fluxes) can be activated setting the \np[=.true.]{ln_mldw}{ln\_mldw} in the namelist. 
    121123 
    122124In this case, the local depth of turbulent wind-mixing or "Ekman depth" $h_{e}(x,y,t)$ is evaluated and 
     
    225227which is valid in a stable stratified region with constant values of the Brunt-Vais\"{a}l\"{a} frequency. 
    226228The resulting length scale is bounded by the distance to the surface or to the bottom 
    227 (\np{nn_mxl}{nn\_mxl}\forcode{=0}) or by the local vertical scale factor (\np{nn_mxl}{nn\_mxl}\forcode{=1}). 
     229(\np[=0]{nn_mxl}{nn\_mxl}) or by the local vertical scale factor (\np[=1]{nn_mxl}{nn\_mxl}). 
    228230\citet{blanke.delecluse_JPO93} notice that this simplification has two major drawbacks: 
    229231it makes no sense for locally unstable stratification and the computation no longer uses all 
    230232the information contained in the vertical density profile. 
    231 To overcome these drawbacks, \citet{madec.delecluse.ea_NPM98} introduces the \np{nn_mxl}{nn\_mxl}\forcode{=2, 3} cases, 
     233To overcome these drawbacks, \citet{madec.delecluse.ea_NPM98} introduces the \np[=2, 3]{nn_mxl}{nn\_mxl} cases, 
    232234which add an extra assumption concerning the vertical gradient of the computed length scale. 
    233235So, the length scales are first evaluated as in \autoref{eq:ZDF_tke_mxl0_1} and then bounded such that: 
     
    267269where $l^{(k)}$ is computed using \autoref{eq:ZDF_tke_mxl0_1}, \ie\ $l^{(k)} = \sqrt {2 {\bar e}^{(k)} / {N^2}^{(k)} }$. 
    268270 
    269 In the \np{nn_mxl}{nn\_mxl}\forcode{=2} case, the dissipation and mixing length scales take the same value: 
    270 $ l_k=  l_\epsilon = \min \left(\ l_{up} \;,\;  l_{dwn}\ \right)$, while in the \np{nn_mxl}{nn\_mxl}\forcode{=3} case, 
     271In the \np[=2]{nn_mxl}{nn\_mxl} case, the dissipation and mixing length scales take the same value: 
     272$ l_k=  l_\epsilon = \min \left(\ l_{up} \;,\;  l_{dwn}\ \right)$, while in the \np[=3]{nn_mxl}{nn\_mxl} case, 
    271273the dissipation and mixing turbulent length scales are give as in \citet{gaspar.gregoris.ea_JGR90}: 
    272274\[ 
     
    312314$\alpha_{CB} = 100$ the Craig and Banner's value. 
    313315As the surface boundary condition on TKE is prescribed through $\bar{e}_o = e_{bb} |\tau| / \rho_o$, 
    314 with $e_{bb}$ the \np{rn_ebb}{rn\_ebb} namelist parameter, setting \np{rn_ebb}{rn\_ebb}\forcode{ = 67.83} corresponds 
     316with $e_{bb}$ the \np{rn_ebb}{rn\_ebb} namelist parameter, setting \np[=67.83]{rn_ebb}{rn\_ebb} corresponds 
    315317to $\alpha_{CB} = 100$. 
    316 Further setting  \np{ln_mxl0}{ln\_mxl0}\forcode{ =.true.},  applies \autoref{eq:ZDF_Lsbc} as the surface boundary condition on the length scale, 
     318Further setting  \np[=.true.]{ln_mxl0}{ln\_mxl0},  applies \autoref{eq:ZDF_Lsbc} as the surface boundary condition on the length scale, 
    317319with $\beta$ hard coded to the Stacey's value. 
    318320Note that a minimal threshold of \np{rn_emin0}{rn\_emin0}$=10^{-4}~m^2.s^{-2}$ (namelist parameters) is applied on the 
     
    385387(\ie\ near-inertial oscillations and ocean swells and waves). 
    386388 
    387 When using this parameterization (\ie\ when \np{nn_etau}{nn\_etau}\forcode{=1}), 
     389When using this parameterization (\ie\ when \np[=1]{nn_etau}{nn\_etau}), 
    388390the TKE input to the ocean ($S$) imposed by the winds in the form of near-inertial oscillations, 
    389391swell and waves is parameterized by \autoref{eq:ZDF_Esbc} the standard TKE surface boundary condition, 
     
    398400(no penetration if $f_i=1$, \ie\ if the ocean is entirely covered by sea-ice). 
    399401The value of $f_r$, usually a few percents, is specified through \np{rn_efr}{rn\_efr} namelist parameter. 
    400 The vertical mixing length scale, $h_\tau$, can be set as a 10~m uniform value (\np{nn_etau}{nn\_etau}\forcode{=0}) or 
     402The vertical mixing length scale, $h_\tau$, can be set as a 10~m uniform value (\np[=0]{nn_etau}{nn\_etau}) or 
    401403a latitude dependent value (varying from 0.5~m at the Equator to a maximum value of 30~m at high latitudes 
    402 (\np{nn_etau}{nn\_etau}\forcode{=1}). 
    403  
    404 Note that two other option exist, \np{nn_etau}{nn\_etau}\forcode{=2, 3}. 
     404(\np[=1]{nn_etau}{nn\_etau}). 
     405 
     406Note that two other option exist, \np[=2, 3]{nn_etau}{nn\_etau}. 
    405407They correspond to applying \autoref{eq:ZDF_Ehtau} only at the base of the mixed layer, 
    406408or to using the high frequency part of the stress to evaluate the fraction of TKE that penetrates the ocean. 
     
    508510  \caption[Set of predefined GLS parameters or equivalently predefined turbulence models available]{ 
    509511    Set of predefined GLS parameters, or equivalently predefined turbulence models available with 
    510     \protect\np{ln_zdfgls}{ln\_zdfgls}\forcode{=.true.} and controlled by 
     512    \protect\np[=.true.]{ln_zdfgls}{ln\_zdfgls} and controlled by 
    511513    the \protect\np{nn_clos}{nn\_clos} namelist variable in \protect\nam{zdf_gls}{zdf\_gls}.} 
    512514  \label{tab:ZDF_GLS} 
     
    519521$C_{\mu}$ and $C_{\mu'}$ are calculated from stability function proposed by \citet{galperin.kantha.ea_JAS88}, 
    520522or by \citet{kantha.clayson_JGR94} or one of the two functions suggested by \citet{canuto.howard.ea_JPO01} 
    521 (\np{nn_stab_func}{nn\_stab\_func}\forcode{=0, 3}, resp.). 
     523(\np[=0, 3]{nn_stab_func}{nn\_stab\_func}, resp.). 
    522524The value of $C_{0\mu}$ depends on the choice of the stability function. 
    523525 
     
    525527Neumann condition through \np{nn_bc_surf}{nn\_bc\_surf} and \np{nn_bc_bot}{nn\_bc\_bot}, resp. 
    526528As for TKE closure, the wave effect on the mixing is considered when 
    527 \np{rn_crban}{rn\_crban}\forcode{ > 0.} \citep{craig.banner_JPO94, mellor.blumberg_JPO04}. 
     529\np[ > 0.]{rn_crban}{rn\_crban} \citep{craig.banner_JPO94, mellor.blumberg_JPO04}. 
    528530The \np{rn_crban}{rn\_crban} namelist parameter is $\alpha_{CB}$ in \autoref{eq:ZDF_Esbc} and 
    529531\np{rn_charn}{rn\_charn} provides the value of $\beta$ in \autoref{eq:ZDF_Lsbc}. 
     
    536538the entrainment depth predicted in stably stratified situations, 
    537539and that its value has to be chosen in accordance with the algebraic model for the turbulent fluxes. 
    538 The clipping is only activated if \np{ln_length_lim}{ln\_length\_lim}\forcode{=.true.}, 
     540The clipping is only activated if \np[=.true.]{ln_length_lim}{ln\_length\_lim}, 
    539541and the $c_{lim}$ is set to the \np{rn_clim_galp}{rn\_clim\_galp} value. 
    540542 
     
    707709 
    708710Options are defined through the \nam{zdf}{zdf} namelist variables. 
    709 The non-penetrative convective adjustment is used when \np{ln_zdfnpc}{ln\_zdfnpc}\forcode{=.true.}. 
     711The non-penetrative convective adjustment is used when \np[=.true.]{ln_zdfnpc}{ln\_zdfnpc}. 
    710712It is applied at each \np{nn_npc}{nn\_npc} time step and mixes downwards instantaneously the statically unstable portion of 
    711713the water column, but only until the density structure becomes neutrally stable 
     
    751753 
    752754Options are defined through the  \nam{zdf}{zdf} namelist variables. 
    753 The enhanced vertical diffusion parameterisation is used when \np{ln_zdfevd}{ln\_zdfevd}\forcode{=.true.}. 
     755The enhanced vertical diffusion parameterisation is used when \np[=.true.]{ln_zdfevd}{ln\_zdfevd}. 
    754756In this case, the vertical eddy mixing coefficients are assigned very large values 
    755757in regions where the stratification is unstable 
    756758(\ie\ when $N^2$ the Brunt-Vais\"{a}l\"{a} frequency is negative) \citep{lazar_phd97, lazar.madec.ea_JPO99}. 
    757 This is done either on tracers only (\np{nn_evdm}{nn\_evdm}\forcode{=0}) or 
    758 on both momentum and tracers (\np{nn_evdm}{nn\_evdm}\forcode{=1}). 
    759  
    760 In practice, where $N^2\leq 10^{-12}$, $A_T^{vT}$ and $A_T^{vS}$, and if \np{nn_evdm}{nn\_evdm}\forcode{=1}, 
     759This is done either on tracers only (\np[=0]{nn_evdm}{nn\_evdm}) or 
     760on both momentum and tracers (\np[=1]{nn_evdm}{nn\_evdm}). 
     761 
     762In practice, where $N^2\leq 10^{-12}$, $A_T^{vT}$ and $A_T^{vS}$, and if \np[=1]{nn_evdm}{nn\_evdm}, 
    761763the four neighbouring $A_u^{vm} \;\mbox{and}\;A_v^{vm}$ values also, are set equal to 
    762764the namelist parameter \np{rn_avevd}{rn\_avevd}. 
     
    795797The OSMOSIS turbulent closure scheme already includes enhanced vertical diffusion in the case of convection, 
    796798%as governed by the variables $bvsqcon$ and $difcon$ found in \mdl{zdfkpp}, 
    797 therefore \np{ln_zdfevd}{ln\_zdfevd}\forcode{=.false.} should be used with the OSMOSIS scheme. 
     799therefore \np[=.false.]{ln_zdfevd}{ln\_zdfevd} should be used with the OSMOSIS scheme. 
    798800% gm%  + one word on non local flux with KPP scheme trakpp.F90 module... 
    799801 
     
    10021004    c_b^T = - r 
    10031005\] 
    1004 When \np{ln_lin}{ln\_lin} \forcode{= .true.}, the value of $r$ used is \np{rn_Uc0}{rn\_Uc0}*\np{rn_Cd0}{rn\_Cd0}. 
    1005 Setting \np{ln_OFF}{ln\_OFF} \forcode{= .true.} (and \forcode{ln_lin=.true.}) is equivalent to setting $r=0$ and leads to a free-slip boundary condition. 
     1006When \np[=.true.]{ln_lin}{ln\_lin}, the value of $r$ used is \np{rn_Uc0}{rn\_Uc0}*\np{rn_Cd0}{rn\_Cd0}. 
     1007Setting \np[=.true.]{ln_OFF}{ln\_OFF} (and \forcode{ln_lin=.true.}) is equivalent to setting $r=0$ and leads to a free-slip boundary condition. 
    10061008 
    10071009These values are assigned in \mdl{zdfdrg}. 
    10081010Note that there is support for local enhancement of these values via an externally defined 2D mask array 
    1009 (\np{ln_boost}{ln\_boost}\forcode{=.true.}) given in the \ifile{bfr\_coef} input NetCDF file. 
     1011(\np[=.true.]{ln_boost}{ln\_boost}) given in the \ifile{bfr\_coef} input NetCDF file. 
    10101012The mask values should vary from 0 to 1. 
    10111013Locations with a non-zero mask value will have the friction coefficient increased by 
     
    10431045$C_D$= \np{rn_Cd0}{rn\_Cd0}, and $e_b$ =\np{rn_bfeb2}{rn\_bfeb2}. 
    10441046Note that for applications which consider tides explicitly, a low or even zero value of \np{rn_bfeb2}{rn\_bfeb2} is recommended. A local enhancement of $C_D$ is again possible via an externally defined 2D mask array 
    1045 (\np{ln_boost}{ln\_boost}\forcode{=.true.}). 
     1047(\np[=.true.]{ln_boost}{ln\_boost}). 
    10461048This works in the same way as for the linear friction case with non-zero masked locations increased by 
    10471049$mask\_value$ * \np{rn_boost}{rn\_boost} * \np{rn_Cd0}{rn\_Cd0}. 
     
    10551057In the non-linear friction case, the drag coefficient, $C_D$, can be optionally enhanced using 
    10561058a "law of the wall" scaling. This assumes that the model vertical resolution can capture the logarithmic layer which typically occur for layers thinner than 1 m or so. 
    1057 If  \np{ln_loglayer}{ln\_loglayer} \forcode{= .true.}, $C_D$ is no longer constant but is related to the distance to the wall (or equivalently to the half of the top/bottom layer thickness): 
     1059If  \np[=.true.]{ln_loglayer}{ln\_loglayer}, $C_D$ is no longer constant but is related to the distance to the wall (or equivalently to the half of the top/bottom layer thickness): 
    10581060\[ 
    10591061  C_D = \left ( {\kappa \over {\mathrm log}\left ( 0.5 \; e_{3b} / rn\_{z0} \right ) } \right )^2 
     
    10701072 
    10711073\noindent The log-layer enhancement can also be applied to the top boundary friction if 
    1072 under ice-shelf cavities are activated (\np{ln_isfcav}{ln\_isfcav}\forcode{=.true.}). 
     1074under ice-shelf cavities are activated (\np[=.true.]{ln_isfcav}{ln\_isfcav}). 
    10731075%In this case, the relevant namelist parameters are \np{rn_tfrz0}{rn\_tfrz0}, \np{rn_tfri2}{rn\_tfri2} and \np{rn_tfri2_max}{rn\_tfri2\_max}. 
    10741076 
     
    10761078%       Explicit bottom Friction 
    10771079% ------------------------------------------------------------------------------------------------------------- 
    1078 \subsection[Explicit top/bottom friction (\forcode{ln_drgimp=.false.})]{Explicit top/bottom friction (\protect\np{ln_drgimp}{ln\_drgimp}\forcode{=.false.})} 
     1080\subsection[Explicit top/bottom friction (\forcode{ln_drgimp=.false.})]{Explicit top/bottom friction (\protect\np[=.false.]{ln_drgimp}{ln\_drgimp})} 
    10791081\label{subsec:ZDF_drg_stability} 
    10801082 
    1081 Setting \np{ln_drgimp}{ln\_drgimp} \forcode{= .false.} means that bottom friction is treated explicitly in time, which has the advantage of simplifying the interaction with the split-explicit free surface (see \autoref{subsec:ZDF_drg_ts}). The latter does indeed require the knowledge of bottom stresses in the course of the barotropic sub-iteration, which becomes less straightforward in the implicit case. In the explicit case, top/bottom stresses can be computed using \textit{before} velocities and inserted in the overall momentum tendency budget. This reads: 
     1083Setting \np[=.false.]{ln_drgimp}{ln\_drgimp} means that bottom friction is treated explicitly in time, which has the advantage of simplifying the interaction with the split-explicit free surface (see \autoref{subsec:ZDF_drg_ts}). The latter does indeed require the knowledge of bottom stresses in the course of the barotropic sub-iteration, which becomes less straightforward in the implicit case. In the explicit case, top/bottom stresses can be computed using \textit{before} velocities and inserted in the overall momentum tendency budget. This reads: 
    10821084 
    10831085At the top (below an ice shelf cavity): 
     
    11371139%       Implicit Bottom Friction 
    11381140% ------------------------------------------------------------------------------------------------------------- 
    1139 \subsection[Implicit top/bottom friction (\forcode{ln_drgimp=.true.})]{Implicit top/bottom friction (\protect\np{ln_drgimp}{ln\_drgimp}\forcode{=.true.})} 
     1141\subsection[Implicit top/bottom friction (\forcode{ln_drgimp=.true.})]{Implicit top/bottom friction (\protect\np[=.true.]{ln_drgimp}{ln\_drgimp})} 
    11401142\label{subsec:ZDF_drg_imp} 
    11411143 
     
    11701172\label{subsec:ZDF_drg_ts} 
    11711173 
    1172 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. 
     1174With 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[=.false.]{ln_drgimp}{ln\_drgimp} 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[=.true.]{ln_drgimp}{ln\_drgimp},  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. 
    11731175 
    11741176The strategy to handle top/bottom stresses with split-explicit free surface in \NEMO\ is as follows: 
     
    15081510% ================================================================ 
    15091511 
    1510 \biblio 
    1511  
    1512 \pindex 
     1512\onlyinsubfile{\bibliography{../main/bibliography}} 
     1513 
     1514\onlyinsubfile{\printindex} 
    15131515 
    15141516\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_cfgs.tex

    r11578 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    253255 
    254256The GYRE configuration is set like an analytical configuration. 
    255 Through \np{ln_read_cfg}{ln\_read\_cfg}\forcode{ = .false.} in \nam{cfg}{cfg} namelist defined in 
     257Through \np[=.false.]{ln_read_cfg}{ln\_read\_cfg} in \nam{cfg}{cfg} namelist defined in 
    256258the reference configuration \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg} 
    257259analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines. 
     
    271273For example, keeping a same model size on each processor while increasing the number of processor used is very easy, 
    272274even though the physical integrity of the solution can be compromised. 
    273 Benchmark is activate via \np{ln_bench}{ln\_bench}\forcode{ = .true.} in \nam{usr_def}{usr\_def} in 
     275Benchmark is activate via \np[=.true.]{ln_bench}{ln\_bench} in \nam{usr_def}{usr\_def} in 
    274276namelist \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}. 
    275277 
     
    299301In particular, the AMM uses $s$-coordinates in the vertical rather than $z$-coordinates and 
    300302is forced with tidal lateral boundary conditions using a Flather boundary condition from the BDY module. 
    301 Also specific to the AMM configuration is the use of the GLS turbulence scheme (\np{ln_zdfgls}{ln\_zdfgls} \forcode{= .true.}). 
     303Also specific to the AMM configuration is the use of the GLS turbulence scheme (\np[=.true.]{ln_zdfgls}{ln\_zdfgls}). 
    302304 
    303305In addition to the tidal boundary condition the model may also take open boundary conditions from 
     
    308310Unlike ordinary river points the Baltic inputs also include salinity and temperature data. 
    309311 
    310 \biblio 
    311  
    312 \pindex 
     312\onlyinsubfile{\bibliography{../main/bibliography}} 
     313 
     314\onlyinsubfile{\printindex} 
    313315 
    314316\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_conservation.tex

    r11544 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
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     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    329331It has not been implemented. 
    330332 
    331 \biblio 
    332  
    333 \pindex 
     333\onlyinsubfile{\bibliography{../main/bibliography}} 
     334 
     335\onlyinsubfile{\printindex} 
    334336 
    335337\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex

    r11578 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
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     3\onlyinsubfile{\makeindex} 
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    35\begin{document} 
     
    416418 
    417419% ================================================================ 
    418 \biblio 
    419  
    420 \pindex 
     420\onlyinsubfile{\bibliography{../main/bibliography}} 
     421 
     422\onlyinsubfile{\printindex} 
    421423 
    422424\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics.tex

    r11561 r11582  
    11731173Nevertheless it is currently not available in the iso-neutral case. 
    11741174 
    1175 \biblio 
    1176  
    1177 \pindex 
     1175\onlyinsubfile{\bibliography{../main/bibliography}} 
     1176 
     1177\onlyinsubfile{\input{../../global/printindex}} 
    11781178 
    11791179\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

    r11578 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\onlyinsubfile{\makeindex} 
    24 
    35\begin{document} 
     
    299301The default value is 1, as recommended by \citet{Roullet2000?} 
    300302 
    301 \colorbox{red}{\np{rnu}{rnu}\forcode{=1} to be suppressed from namelist !} 
     303\colorbox{red}{\np[=1]{rnu}{rnu} to be suppressed from namelist !} 
    302304 
    303305%------------------------------------------------------------- 
     
    313315In particular, this means that in filtered case, the matrix to be inverted has to be recomputed at each time-step. 
    314316 
    315 \biblio 
    316  
    317 \pindex 
     317\onlyinsubfile{\bibliography{../main/bibliography}} 
     318 
     319\onlyinsubfile{\printindex} 
    318320 
    319321\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex

    r11578 r11582  
    11\documentclass[../main/NEMO_manual]{subfiles} 
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    35\begin{document} 
     
    8688where the subscript $F$ denotes filtered values and $\gamma$ is the Asselin coefficient. 
    8789$\gamma$ is initialized as \np{rn_atfp}{rn\_atfp} (namelist parameter). 
    88 Its default value is \np{rn_atfp}{rn\_atfp}\forcode{ = 10.e-3} (see \autoref{sec:TD_mLF}), 
     90Its default value is \np[=10.e-3]{rn_atfp}{rn\_atfp} (see \autoref{sec:TD_mLF}), 
    8991causing only a weak dissipation of high frequency motions (\citep{farge-coulombier_phd87}). 
    9092The addition of a time filter degrades the accuracy of the calculation from second to first order. 
     
    172174 
    173175The leapfrog environment supports a centred in time computation of the surface pressure, \ie\ evaluated 
    174 at \textit{now} time step. This refers to as the explicit free surface case in the code (\np{ln_dynspg_exp}{ln\_dynspg\_exp}\forcode{=.true.}). 
     176at \textit{now} time step. This refers to as the explicit free surface case in the code (\np[=.true.]{ln_dynspg_exp}{ln\_dynspg\_exp}). 
    175177This choice however imposes a strong constraint on the time step which should be small enough to resolve the propagation 
    176178of external gravity waves. As a matter of fact, one rather use in a realistic setup, a split-explicit free surface 
    177 (\np{ln_dynspg_ts}{ln\_dynspg\_ts}\forcode{=.true.}) in which barotropic and baroclinic dynamical equations are solved separately with ad-hoc 
     179(\np[=.true.]{ln_dynspg_ts}{ln\_dynspg\_ts}) in which barotropic and baroclinic dynamical equations are solved separately with ad-hoc 
    178180time steps. The use of the time-splitting (in combination with non-linear free surface) imposes some constraints on the design of 
    179181the overall flowchart, in particular to ensure exact tracer conservation (see \autoref{fig:TD_TimeStep_flowchart}). 
     
    297299When restarting, if the time step has been changed, or one of the prognostic variables at \textit{before} time step 
    298300is missing, an Euler time stepping scheme is imposed. A forward initial step can still be enforced by the user by setting 
    299 the namelist variable \np{nn_euler}{nn\_euler}\forcode{=0}. Other options to control the time integration of the model 
     301the namelist variable \np[=0]{nn_euler}{nn\_euler}. Other options to control the time integration of the model 
    300302are defined through the  \nam{run}{run} namelist variables. 
    301303%%% 
     
    386388} 
    387389 
    388 \biblio 
    389  
    390 \pindex 
     390\onlyinsubfile{\bibliography{../main/bibliography}} 
     391 
     392\onlyinsubfile{\printindex} 
    391393 
    392394\end{document} 
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