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Changeset 11582 – NEMO

# Changeset 11582

Ignore:
Timestamp:
2019-09-20T11:44:31+02:00 (3 years ago)
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

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

 r11578 \documentclass[../main/NEMO_manual]{subfiles} \onlyinsubfile{\makeindex} \begin{document} \begin{description} \item[\np{jphgr_mesh}{jphgr\_mesh}=0]  The most general curvilinear orthogonal grids. \item[{\np{jphgr_mesh}{jphgr\_mesh}=0}]  The most general curvilinear orthogonal grids. The coordinates and their first derivatives with respect to $i$ and $j$ are provided in a input file (\ifile{coordinates}), read in \rou{hgr\_read} subroutine of the domhgr module. This is now the only option available within \NEMO\ itself from v4.0 onwards. \item[\np{jphgr_mesh}{jphgr\_mesh}=1 to 5] A few simple analytical grids are provided (see below). \item[{\np{jphgr_mesh}{jphgr\_mesh}=1 to 5}] A few simple analytical grids are provided (see below). For other analytical grids, the \mdl{domhgr} module (\texttt{DOMAINcfg} variant) must be modified by the user. In most cases, modifying the \mdl{usrdef\_hgr} module of \NEMO\ is It is possible to define a simple regular vertical grid by giving zero stretching (\np{ppacr}{ppacr}\forcode{ = 0}).  In that case, the parameters \jp{jpk} (number of $w$-levels) (\np[=0]{ppacr}{ppacr}).  In that case, the parameters \jp{jpk} (number of $w$-levels) and \np{pphmax}{pphmax} (total ocean depth in meters) fully define the grid. top and bottom with a smooth hyperbolic tangent transition in between (\autoref{fig:DOMCFG_zgr}). A double hyperbolic tangent version (\np{ldbletanh}{ldbletanh}\forcode{ = .true.}) is also available A double hyperbolic tangent version (\np[=.true.]{ldbletanh}{ldbletanh}) is also available which permits finer control and is used, typically, to obtain a well resolved upper ocean without compromising on resolution at depth using a moderate number of levels. \end{gather} If the ice shelf cavities are opened (\np{ln_isfcav}{ln\_isfcav}\forcode{ = .true.}), the definition If the ice shelf cavities are opened (\np[=.true.]{ln_isfcav}{ln\_isfcav}), the definition of $z_0$ is the same.  However, definition of $e_3^0$ at $t$- and $w$-points is respectively changed to: \np{nn_bathy}{nn\_bathy} (found in \nam{dom}{dom} namelist (\texttt{DOMAINCFG} variant) ): \begin{description} \item[\np{nn_bathy}{nn\_bathy}\forcode{ = 0}]: \item[{\np[=0]{nn_bathy}{nn\_bathy}}]: a flat-bottom domain is defined. The total depth $z_w (jpk)$ is given by the coordinate transformation. The domain can either be a closed basin or a periodic channel depending on the parameter \np{jperio}{jperio}. \item[\np{nn_bathy}{nn\_bathy}\forcode{ = -1}]: \item[{\np[=-1]{nn_bathy}{nn\_bathy}}]: a domain with a bump of topography one third of the domain width at the central latitude. This is meant for the "EEL-R5" configuration, a periodic or open boundary channel with a seamount. \item[\np{nn_bathy}{nn\_bathy}\forcode{ = 1}]: \item[{\np[=1]{nn_bathy}{nn\_bathy}}]: read a bathymetry and ice shelf draft (if needed). The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters) at The \ifile{isfdraft\_meter} file (Netcdf format) provides the ice shelf draft (positive, in meters) at each grid point of the model grid. This file is only needed if \np{ln_isfcav}{ln\_isfcav}\forcode{ = .true.}. This file is only needed if \np[=.true.]{ln_isfcav}{ln\_isfcav}. Defining the ice shelf draft will also define the ice shelf edge and the grounding line position. \end{description} %-------------------------------------------------------------------------------------------------------------- Options are defined in \nam{zgr_sco}{zgr\_sco} (\texttt{DOMAINcfg} only). In $s$-coordinate (\np{ln_sco}{ln\_sco}\forcode{ = .true.}), the depth and thickness of the model levels are defined from In $s$-coordinate (\np[=.true.]{ln_sco}{ln\_sco}), the depth and thickness of the model levels are defined from the product of a depth field and either a stretching function or its derivative, respectively: The original default \NEMO\ s-coordinate stretching is available if neither of the other options are specified as true (\np{ln_s_SH94}{ln\_s\_SH94}\forcode{ = .false.} and \np{ln_s_SF12}{ln\_s\_SF12}\forcode{ = .false.}). (\np[=.false.]{ln_s_SH94}{ln\_s\_SH94} and \np[=.false.]{ln_s_SF12}{ln\_s\_SF12}). This uses a depth independent $\tanh$ function for the stretching \citep{madec.delecluse.ea_JPO96}: A stretching function, modified from the commonly used \citet{song.haidvogel_JCP94} stretching (\np{ln_s_SH94}{ln\_s\_SH94}\forcode{ = .true.}), modified from the commonly used \citet{song.haidvogel_JCP94} stretching (\np[=.true.]{ln_s_SH94}{ln\_s\_SH94}), is also available and is more commonly used for shelf seas modelling: This option is described in the Report by Levier \textit{et al.} (2007), available on the \NEMO\ web site. \biblio \pindex \onlyinsubfile{\bibliography{../main/bibliography}} \onlyinsubfile{\printindex} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/apdx_algos.tex

 r11577 \documentclass[../main/NEMO_manual]{subfiles} \onlyinsubfile{\makeindex} \begin{document} %        UBS scheme % ------------------------------------------------------------------------------------------------------------- \section{Upstream Biased Scheme (UBS) (\protect\np{ln_traadv_ubs}{ln\_traadv\_ubs}\forcode{ = .true.})} \section{Upstream Biased Scheme (UBS) (\protect\np[=.true.]{ln_traadv_ubs}{ln\_traadv\_ubs})} \label{sec:ALGOS_tra_adv_ubs} the control of artificial diapycnal fluxes is of paramount importance. It has therefore been preferred to evaluate the vertical flux using the TVD scheme when \np{ln_traadv_ubs}{ln\_traadv\_ubs}\forcode{ = .true.}. \np[=.true.]{ln_traadv_ubs}{ln\_traadv\_ubs}. For stability reasons, in \autoref{eq:TRA_adv_ubs}, the first term which corresponds to \ie\ the variance of the tracer is preserved by the discretisation of the skew fluxes. \biblio \pindex \onlyinsubfile{\bibliography{../main/bibliography}} \onlyinsubfile{\printindex} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/apdx_diff_opers.tex

 r11558 \documentclass[../main/NEMO_manual]{subfiles} \onlyinsubfile{\makeindex} \begin{document} that is a Laplacian diffusion is applied on momentum along the coordinate directions. \biblio \pindex \onlyinsubfile{\bibliography{../main/bibliography}} \onlyinsubfile{\printindex} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/apdx_invariants.tex

 r11577 \documentclass[../main/NEMO_manual]{subfiles} \onlyinsubfile{\makeindex} \begin{document} %       Vorticity Term with ENE scheme % ------------------------------------------------------------------------------------------------------------- \subsubsection{Vorticity term with ENE scheme (\protect\np{ln_dynvor_ene}{ln\_dynvor\_ene}\forcode{ = .true.})} \subsubsection{Vorticity term with ENE scheme (\protect\np[=.true.]{ln_dynvor_ene}{ln\_dynvor\_ene})} \label{subsec:INVARIANTS_vorENE} %       Vorticity Term with EEN scheme % ------------------------------------------------------------------------------------------------------------- \subsubsection{Vorticity term with EEN scheme (\protect\np{ln_dynvor_een}{ln\_dynvor\_een}\forcode{ = .true.})} \subsubsection{Vorticity term with EEN scheme (\protect\np[=.true.]{ln_dynvor_een}{ln\_dynvor\_een})} \label{subsec:INVARIANTS_vorEEN_vect} %       Vorticity Term with ENS scheme % ------------------------------------------------------------------------------------------------------------- \subsubsection{Vorticity term with ENS scheme  (\protect\np{ln_dynvor_ens}{ln\_dynvor\_ens}\forcode{ = .true.})} \subsubsection{Vorticity term with ENS scheme  (\protect\np[=.true.]{ln_dynvor_ens}{ln\_dynvor\_ens})} \label{subsec:INVARIANTS_vorENS} %       Vorticity Term with EEN scheme % ------------------------------------------------------------------------------------------------------------- \subsubsection{Vorticity Term with EEN scheme (\protect\np{ln_dynvor_een}{ln\_dynvor\_een}\forcode{ = .true.})} \subsubsection{Vorticity Term with EEN scheme (\protect\np[=.true.]{ln_dynvor_een}{ln\_dynvor\_een})} \label{subsec:INVARIANTS_vorEEN} %%%%  end of appendix in gm comment %} \biblio \pindex \onlyinsubfile{\bibliography{../main/bibliography}} \onlyinsubfile{\printindex} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/apdx_s_coord.tex

 r11558 \documentclass[../main/NEMO_manual]{subfiles} \onlyinsubfile{\makeindex} \begin{document} the expression of the 3D divergence in the $s-$coordinates established above. \biblio \pindex \onlyinsubfile{\bibliography{../main/bibliography}} \onlyinsubfile{\printindex} \end{document}

 r11577 \newcommand{\rtriadt}[1]{\ensuremath{\triadt{i}{k}{#1}{i_p}{k_p}}} \onlyinsubfile{\makeindex} \begin{document} % ================================================================ The options specific to the Griffies scheme include: \begin{description} \item[\np{ln_triad_iso}{ln\_triad\_iso}] \item[{\np{ln_triad_iso}{ln\_triad\_iso}}] See \autoref{sec:TRIADS_taper}. If this is set false (the default), giving an almost pure horizontal diffusive tracer flux within the mixed layer. This is similar to the tapering suggested by \citet{gerdes.koberle.ea_CD91}. See \autoref{subsec:TRIADS_Gerdes-taper} \item[\np{ln_botmix_triad}{ln\_botmix\_triad}] \item[{\np{ln_botmix_triad}{ln\_botmix\_triad}}] See \autoref{sec:TRIADS_iso_bdry}. If this is set false (the default) then the lateral diffusive fluxes If it is set true, however, then these lateral diffusive fluxes are applied, giving smoother bottom tracer fields at the cost of introducing diapycnal mixing. \item[\np{rn_sw_triad}{rn\_sw\_triad}] \item[{\np{rn_sw_triad}{rn\_sw\_triad}}] blah blah to be added.... \end{description} The options shared with the Standard scheme include: \begin{description} \item[\np{ln_traldf_msc}{ln\_traldf\_msc}]   blah blah to be added \item[\np{rn_slpmax}{rn\_slpmax}]  blah blah to be added \item[{\np{ln_traldf_msc}{ln\_traldf\_msc}}]   blah blah to be added \item[{\np{rn_slpmax}{rn\_slpmax}}]  blah blah to be added \end{description} Note 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 either of the $i,k+1$ or $i+1,k+1$ tracer points is masked, \ie\ the $i,k+1$ $u$-point is masked. The associated lateral fluxes (grey-black dashed line) are masked if \np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .false.}, but left unmasked, giving bottom mixing, if \np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .true.}. The default option \np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .false.} is suitable when the bbl mixing option is enabled (\np{ln_trabbl}{ln\_trabbl}\forcode{ = .true.}, with \np{nn_bbl_ldf}{nn\_bbl\_ldf}\forcode{ = 1}), or for simple idealized problems. For setups with topography without bbl mixing, \np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .true.} may be necessary. The associated lateral fluxes (grey-black dashed line) are masked if \np[=.false.]{ln_botmix_triad}{ln\_botmix\_triad}, but left unmasked, giving bottom mixing, if \np[=.true.]{ln_botmix_triad}{ln\_botmix\_triad}. The default option \np[=.false.]{ln_botmix_triad}{ln\_botmix\_triad} is suitable when the bbl mixing option is enabled (\np[=.true.]{ln_trabbl}{ln\_trabbl}, with \np[=1]{nn_bbl_ldf}{nn\_bbl\_ldf}), or for simple idealized problems. For setups with topography without bbl mixing, \np[=.true.]{ln_botmix_triad}{ln\_botmix\_triad} may be necessary. % >>>>>>>>>>>>>>>>>>>>>>>>>>>> \begin{figure}[h] \ie\ the $i,k+1$ $u$-point is masked. The associated lateral fluxes (grey-black dashed line) are masked if \protect\np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .false.}, but left unmasked, giving bottom mixing, if \protect\np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .true.}} \protect\np[=.false.]{ln_botmix_triad}{ln\_botmix\_triad}, but left unmasked, giving bottom mixing, if \protect\np[=.true.]{ln_botmix_triad}{ln\_botmix\_triad}} \label{fig:TRIADS_bdry_triads} \end{figure} \label{sec:TRIADS_lintaper} This is the option activated by the default choice \np{ln_triad_iso}{ln\_triad\_iso}\forcode{ = .false.}. This is the option activated by the default choice \np[=.false.]{ln_triad_iso}{ln\_triad\_iso}. Slopes $\tilde{r}_i$ relative to geopotentials are tapered linearly from their value immediately below the mixed layer to zero at the surface, as described in option (c) of \autoref{fig:LDF_eiv_slp}, to values \label{sec:TRIADS_sfdiag} Where the namelist parameter \np{ln_traldf_gdia}{ln\_traldf\_gdia}\forcode{ = .true.}, Where the namelist parameter \np[=.true.]{ln_traldf_gdia}{ln\_traldf\_gdia}, diagnosed mean eddy-induced velocities are output. Each time step, streamfunctions are calculated in the $i$-$k$ and $j$-$k$ planes at \] \biblio \pindex \onlyinsubfile{\bibliography{../main/bibliography}} \onlyinsubfile{\printindex} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_ASM.tex

 r11578 \documentclass[../main/NEMO_manual]{subfiles} \onlyinsubfile{\makeindex} \begin{document} \end{clines} \biblio \pindex \onlyinsubfile{\bibliography{../main/bibliography}} \onlyinsubfile{\printindex} \end{document}

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

 r11578 \documentclass[../main/NEMO_manual]{subfiles} \onlyinsubfile{\makeindex} \begin{document} (d) hybrid $s-z$ coordinate, (e) hybrid $s-z$ coordinate with partial step, and (f) same as (e) but in the non-linear free surface (\protect\np{ln_linssh}{ln\_linssh}\forcode{=.false.}). (f) same as (e) but in the non-linear free surface (\protect\np[=.false.]{ln_linssh}{ln\_linssh}). Note that the non-linear free surface can be used with any of the 5 coordinates (a) to (e).} \label{fig:DOM_z_zps_s_sps} \begin{itemize} \item $z$-coordinate with full step bathymetry (\np{ln_zco}{ln\_zco}\forcode{=.true.}), \item $z$-coordinate with partial step ($zps$) bathymetry (\np{ln_zps}{ln\_zps}\forcode{=.true.}), \item Generalized, $s$-coordinate (\np{ln_sco}{ln\_sco}\forcode{=.true.}). \item $z$-coordinate with full step bathymetry (\np[=.true.]{ln_zco}{ln\_zco}), \item $z$-coordinate with partial step ($zps$) bathymetry (\np[=.true.]{ln_zps}{ln\_zps}), \item Generalized, $s$-coordinate (\np[=.true.]{ln_sco}{ln\_sco}). \end{itemize} They are updated at each model time step. The initial fixed reference coordinate system is held in variable names with a $\_0$ suffix. When the linear free surface option is used (\np{ln_linssh}{ln\_linssh}\forcode{=.true.}), When the linear free surface option is used (\np[=.true.]{ln_linssh}{ln\_linssh}), \textit{before}, \textit{now} and \textit{after} arrays are initially set to their reference counterpart and remain fixed. \begin{description} \item[\np{ln_tsd_init}{ln\_tsd\_init}\forcode{= .true.}] \item[{\np[=.true.]{ln_tsd_init}{ln\_tsd\_init}}] Use T and S input files that can be given on the model grid itself or on their native input data grids. In the latter case, the data will be interpolated on-the-fly both in the horizontal and the vertical to the model grid The information relating to the input files are specified in the \np{sn_tem}{sn\_tem} and \np{sn_sal}{sn\_sal} structures. The computation is done in the \mdl{dtatsd} module. \item[\np{ln_tsd_init}{ln\_tsd\_init}\forcode{= .false.}] \item[{\np[=.false.]{ln_tsd_init}{ln\_tsd\_init}}] Initial values for T and S are set via a user supplied \rou{usr\_def\_istate} routine contained in \mdl{userdef\_istate}. The default version sets horizontally uniform T and profiles as used in the GYRE configuration \end{description} \biblio \pindex \onlyinsubfile{\bibliography{../main/bibliography}} \onlyinsubfile{\printindex} \end{document}

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

 r11578 \documentclass[../main/NEMO_manual]{subfiles} \onlyinsubfile{\makeindex} \begin{document} (see the \nam{tra_ldf}{tra\_ldf} and \nam{dyn_ldf}{dyn\_ldf} below). Note that this chapter describes the standard implementation of iso-neutral tracer mixing. Griffies's implementation, which is used if \np{ln_traldf_triad}{ln\_traldf\_triad}\forcode{=.true.}, Griffies's implementation, which is used if \np[=.true.]{ln_traldf_triad}{ln\_traldf\_triad}, is described in \autoref{apdx:TRIADS} \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})} It is possible to run without explicit lateral diffusion on tracers (\protect\np{ln_traldf_OFF}{ln\_traldf\_OFF}\forcode{=.true.}) and/or momentum (\protect\np{ln_dynldf_OFF}{ln\_dynldf\_OFF}\forcode{=.true.}). The latter option is even recommended if using the UBS advection scheme on momentum (\np{ln_dynadv_ubs}{ln\_dynadv\_ubs}\forcode{=.true.}, It is possible to run without explicit lateral diffusion on tracers (\protect\np[=.true.]{ln_traldf_OFF}{ln\_traldf\_OFF}) and/or momentum (\protect\np[=.true.]{ln_dynldf_OFF}{ln\_dynldf\_OFF}). The latter option is even recommended if using the UBS advection scheme on momentum (\np[=.true.]{ln_dynadv_ubs}{ln\_dynadv\_ubs}, see \autoref{subsec:DYN_adv_ubs}) and can be useful for testing purposes. \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})} Setting \protect\np{ln_traldf_lap}{ln\_traldf\_lap}\forcode{=.true.} and/or \protect\np{ln_dynldf_lap}{ln\_dynldf\_lap}\forcode{=.true.} enables Setting \protect\np[=.true.]{ln_traldf_lap}{ln\_traldf\_lap} and/or \protect\np[=.true.]{ln_dynldf_lap}{ln\_dynldf\_lap} enables a second order diffusion on tracers and momentum respectively. Note that in \NEMO\ 4, one can not combine Laplacian and Bilaplacian operators for the same variable. \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})} Setting \protect\np{ln_traldf_blp}{ln\_traldf\_blp}\forcode{=.true.} and/or \protect\np{ln_dynldf_blp}{ln\_dynldf\_blp}\forcode{=.true.} enables Setting \protect\np[=.true.]{ln_traldf_blp}{ln\_traldf\_blp} and/or \protect\np[=.true.]{ln_dynldf_blp}{ln\_dynldf\_blp} enables a fourth order diffusion on tracers and momentum respectively. It is implemented by calling the above Laplacian operator twice. We stress again that from \NEMO\ 4, the simultaneous use Laplacian and Bilaplacian operators is not allowed. %gm%  caution I'm not sure the simplification was a good idea! These slopes are computed once in \rou{ldf\_slp\_init} when \np{ln_sco}{ln\_sco}\forcode{=.true.}, and either \np{ln_traldf_hor}{ln\_traldf\_hor}\forcode{=.true.} or \np{ln_dynldf_hor}{ln\_dynldf\_hor}\forcode{=.true.}. These slopes are computed once in \rou{ldf\_slp\_init} when \np[=.true.]{ln_sco}{ln\_sco}, and either \np[=.true.]{ln_traldf_hor}{ln\_traldf\_hor} or \np[=.true.]{ln_dynldf_hor}{ln\_dynldf\_hor}. \subsection{Slopes for tracer iso-neutral mixing} \item[$s$- or hybrid $s$-$z$- coordinate: ] in the current release of \NEMO, iso-neutral mixing is only employed for $s$-coordinates if the Griffies scheme is used (\np{ln_traldf_triad}{ln\_traldf\_triad}\forcode{=.true.}; the Griffies scheme is used (\np[=.true.]{ln_traldf_triad}{ln\_traldf\_triad}; see \autoref{apdx:TRIADS}). In other words, iso-neutral mixing will only be accurately represented with a linear equation of state (\np{ln_seos}{ln\_seos}\forcode{=.true.}). (\np[=.true.]{ln_seos}{ln\_seos}). In the case of a "true" equation of state, the evaluation of $i$ and $j$ derivatives in \autoref{eq:LDF_slp_iso} will include a pressure dependent part, leading to the wrong evaluation of the neutral slopes. To overcome this problem, several techniques have been proposed in which the numerical schemes of the ocean model are modified \citep{weaver.eby_JPO97, griffies.gnanadesikan.ea_JPO98}. Griffies's scheme is now available in \NEMO\ if \np{ln_traldf_triad}{ln\_traldf\_triad}\forcode{ = .true.}; see \autoref{apdx:TRIADS}. Griffies's scheme is now available in \NEMO\ if \np[=.true.]{ln_traldf_triad}{ln\_traldf\_triad}; see \autoref{apdx:TRIADS}. Here, another strategy is presented \citep{lazar_phd97}: a local filtering of the iso-neutral slopes (made on 9 grid-points) prevents the development of The way the mixing coefficients are set in the reference version can be described as follows: \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})} \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})} Mixing coefficients can be read from file if a particular geographical variation is needed. For example, in the ORCA2 global ocean model, decreases linearly to $A^l$~= 2.10$^3$ m$^2$/s at the equator \citep{madec.delecluse.ea_JPO96, delecluse.madec_icol99}. Similar modified horizontal variations can be found with the Antarctic or Arctic sub-domain options of ORCA2 and ORCA05. The provided fields can either be 2d (\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=-20}, \np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=-20}) or 3d (\np{nn_aht_ijk_t}{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}). The 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}). %-------------------------------------------------TABLE--------------------------------------------------- \hline Namelist parameter                       & Input filename                               & dimensions & variable names                      \\  \hline \np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=-20}      & \forcode{eddy_viscosity_2D.nc }            &     $(i,j)$         & \forcode{ahmt_2d, ahmf_2d}  \\  \hline \np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=-20}           & \forcode{eddy_diffusivity_2D.nc }           &     $(i,j)$         & \forcode{ahtu_2d, ahtv_2d}    \\   \hline \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 \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 \np[=-20]{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}     & \forcode{eddy_viscosity_2D.nc }            &     $(i,j)$         & \forcode{ahmt_2d, ahmf_2d}  \\  \hline \np[=-20]{nn_aht_ijk_t}{nn\_aht\_ijk\_t}           & \forcode{eddy_diffusivity_2D.nc }           &     $(i,j)$           & \forcode{ahtu_2d, ahtv_2d}    \\   \hline \np[=-30]{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}        & \forcode{eddy_viscosity_3D.nc }            &     $(i,j,k)$          & \forcode{ahmt_3d, ahmf_3d}  \\  \hline \np[=-30]{nn_aht_ijk_t}{nn\_aht\_ijk\_t}     & \forcode{eddy_diffusivity_3D.nc }           &     $(i,j,k)$         & \forcode{ahtu_3d, ahtv_3d}    \\   \hline \end{tabular} \caption{Description of expected input files if mixing coefficients are read from NetCDF files} %-------------------------------------------------------------------------------------------------------------- \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})} \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})} If constant, mixing coefficients are set thanks to a velocity and a length scales ($U_{scl}$, $L_{scl}$) such that: $U_{scl}$ 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}. \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})} \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})} In the vertically varying case, a hyperbolic variation of the lateral mixing coefficient is introduced in which This profile is hard coded in module \mdl{ldfc1d\_c2d}, but can be easily modified by users. \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})} \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})} In that case, the horizontal variation of the eddy coefficient depends on the local mesh size and \colorbox{yellow}{CASE \np{nn_aht_ijk_t}{nn\_aht\_ijk\_t} = 21 to be added} \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})} \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})} The 3D space variation of the mixing coefficient is simply the combination of the 1D and 2D cases above, the magnitude of the coefficient. \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})} \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})} In 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 $12$): \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 ?} \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})} \subsection[Deformation rate dependent viscosities (\forcode{nn_ahm_ijk_t=32})]{Deformation rate dependent viscosities (\protect\np[=32]{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t})} This option refers to the \citep{smagorinsky_MW63} scheme which is here implemented for momentum only. Smagorinsky chose as a } When  \citet{gent.mcwilliams_JPO90} diffusion is used (\np{ln_ldfeiv}{ln\_ldfeiv}\forcode{=.true.}), When  \citet{gent.mcwilliams_JPO90} diffusion is used (\np[=.true.]{ln_ldfeiv}{ln\_ldfeiv}), an eddy induced tracer advection term is added, the formulation of which depends on the slopes of iso-neutral surfaces. and the sum \autoref{eq:LDF_slp_geo} + \autoref{eq:LDF_slp_iso} in $s$-coordinates. 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: If isopycnal mixing is used in the standard way, \ie\ \np[=.false.]{ln_traldf_triad}{ln\_traldf\_triad}, the eddy induced velocity is given by: \label{eq:LDF_eiv} \colorbox{yellow}{CASE \np{nn_aei_ijk_t}{nn\_aei\_ijk\_t} = 21 to be added} 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}. In 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}. % ================================================================ %-------------------------------------------------------------------------------------------------------------- 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. If  \np[=.true.]{ln_mle}{ln\_mle} in \nam{tra_mle}{tra\_mle} namelist, a parameterization of the mixing due to unresolved mixed layer instabilities is activated (\citet{foxkemper.ferrari_JPO08}). Additional transport is computed in \rou{ldf\_mle\_trp} and added to the eulerian transport in \rou{tra\_adv} as done for eddy induced advection. \colorbox{yellow}{TBC} \biblio \pindex \onlyinsubfile{\bibliography{../main/bibliography}} \onlyinsubfile{\printindex} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_OBS.tex

 r11578 \documentclass[../main/NEMO_manual]{subfiles} \onlyinsubfile{\makeindex} \begin{document} Values between 0 to 4 are associated with interpolation while values 5 or 6 are associated with averaging. \begin{itemize} \item \np{nn_2dint}{nn\_2dint}\forcode{ = 0}: Distance-weighted interpolation \item \np{nn_2dint}{nn\_2dint}\forcode{ = 1}: Distance-weighted interpolation (small angle) \item \np{nn_2dint}{nn\_2dint}\forcode{ = 2}: Bilinear interpolation (geographical grid) \item \np{nn_2dint}{nn\_2dint}\forcode{ = 3}: Bilinear remapping interpolation (general grid) \item \np{nn_2dint}{nn\_2dint}\forcode{ = 4}: Polynomial interpolation \item \np{nn_2dint}{nn\_2dint}\forcode{ = 5}: Radial footprint averaging with diameter specified in the namelist as \item \np[=0]{nn_2dint}{nn\_2dint}: Distance-weighted interpolation \item \np[=1]{nn_2dint}{nn\_2dint}: Distance-weighted interpolation (small angle) \item \np[=2]{nn_2dint}{nn\_2dint}: Bilinear interpolation (geographical grid) \item \np[=3]{nn_2dint}{nn\_2dint}: Bilinear remapping interpolation (general grid) \item \np[=4]{nn_2dint}{nn\_2dint}: Polynomial interpolation \item \np[=5]{nn_2dint}{nn\_2dint}: Radial footprint averaging with diameter specified in the namelist as \texttt{rn\_[var]\_avglamscl} in degrees or metres (set using \texttt{ln\_[var]\_fp\_indegs}) \item \np{nn_2dint}{nn\_2dint}\forcode{ = 6}: Rectangular footprint averaging with E/W and N/S size specified in \item \np[=6]{nn_2dint}{nn\_2dint}: Rectangular footprint averaging with E/W and N/S size specified in the namelist as \texttt{rn\_[var]\_avglamscl} and \texttt{rn\_[var]\_avgphiscl} in degrees or metres (set using \texttt{ln\_[var]\_fp\_indegs}) %>>>>>>>>>>>>>>>>>>>>>>>>>>>> \biblio \pindex \onlyinsubfile{\bibliography{../main/bibliography}} \onlyinsubfile{\printindex} \end{document}

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

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

 r11544 \documentclass[../main/NEMO_manual]{subfiles} \onlyinsubfile{\makeindex} \begin{document} It has not been implemented. \biblio \pindex \onlyinsubfile{\bibliography{../main/bibliography}} \onlyinsubfile{\printindex} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex

 r11578 \documentclass[../main/NEMO_manual]{subfiles} \onlyinsubfile{\makeindex} \begin{document} % ================================================================ \biblio \pindex \onlyinsubfile{\bibliography{../main/bibliography}} \onlyinsubfile{\printindex} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics.tex

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

 r11578 \documentclass[../main/NEMO_manual]{subfiles} \onlyinsubfile{\makeindex} \begin{document} The default value is 1, as recommended by \citet{Roullet2000?} \colorbox{red}{\np{rnu}{rnu}\forcode{=1} to be suppressed from namelist !} \colorbox{red}{\np[=1]{rnu}{rnu} to be suppressed from namelist !} %------------------------------------------------------------- In particular, this means that in filtered case, the matrix to be inverted has to be recomputed at each time-step. \biblio \pindex \onlyinsubfile{\bibliography{../main/bibliography}} \onlyinsubfile{\printindex} \end{document}
• ## NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex

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