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Changeset 11565 – NEMO

Changeset 11565


Ignore:
Timestamp:
2019-09-18T16:58:58+02:00 (5 years ago)
Author:
nicolasmartin
Message:

Cleaning of section titles

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

Legend:

Unmodified
Added
Removed

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

    r11561 r11565  
    211211%                 enstrophy conserving scheme 
    212212%------------------------------------------------------------- 
    213 \subsubsection[Enstrophy conserving scheme (\forcode{ln_dynvor_ens = .true.})]{Enstrophy conserving scheme (\protect\np{ln\_dynvor\_ens}\forcode{ = .true.})} 
     213\subsubsection[Enstrophy conserving scheme (\forcode{ln_dynvor_ens})]{Enstrophy conserving scheme (\protect\np{ln\_dynvor\_ens})} 
    214214\label{subsec:DYN_vor_ens} 
    215215 
    … …  
    234234%                 energy conserving scheme 
    235235%------------------------------------------------------------- 
    236 \subsubsection[Energy conserving scheme (\forcode{ln_dynvor_ene = .true.})]{Energy conserving scheme (\protect\np{ln\_dynvor\_ene}\forcode{ = .true.})} 
     236\subsubsection[Energy conserving scheme (\forcode{ln_dynvor_ene})]{Energy conserving scheme (\protect\np{ln\_dynvor\_ene})} 
    237237\label{subsec:DYN_vor_ene} 
    238238 
    … …  
    254254%                 mix energy/enstrophy conserving scheme 
    255255%------------------------------------------------------------- 
    256 \subsubsection[Mixed energy/enstrophy conserving scheme (\forcode{ln_dynvor_mix = .true.})]{Mixed energy/enstrophy conserving scheme (\protect\np{ln\_dynvor\_mix}\forcode{ = .true.})} 
     256\subsubsection[Mixed energy/enstrophy conserving scheme (\forcode{ln_dynvor_mix})]{Mixed energy/enstrophy conserving scheme (\protect\np{ln\_dynvor\_mix})} 
    257257\label{subsec:DYN_vor_mix} 
    258258 
    … …  
    279279%                 energy and enstrophy conserving scheme 
    280280%------------------------------------------------------------- 
    281 \subsubsection[Energy and enstrophy conserving scheme (\forcode{ln_dynvor_een = .true.})]{Energy and enstrophy conserving scheme (\protect\np{ln\_dynvor\_een}\forcode{ = .true.})} 
     281\subsubsection[Energy and enstrophy conserving scheme (\forcode{ln_dynvor_een})]{Energy and enstrophy conserving scheme (\protect\np{ln\_dynvor\_een})} 
    282282\label{subsec:DYN_vor_een} 
    283283 
    … …  
    489489%                 2nd order centred scheme 
    490490%------------------------------------------------------------- 
    491 \subsubsection[CEN2: $2^{nd}$ order centred scheme (\forcode{ln_dynadv_cen2 = .true.})]{CEN2: $2^{nd}$ order centred scheme (\protect\np{ln\_dynadv\_cen2}\forcode{ = .true.})} 
     491\subsubsection[CEN2: $2^{nd}$ order centred scheme (\forcode{ln_dynadv_cen2})]{CEN2: $2^{nd}$ order centred scheme (\protect\np{ln\_dynadv\_cen2})} 
    492492\label{subsec:DYN_adv_cen2} 
    493493 
    … …  
    512512%                 UBS scheme 
    513513%------------------------------------------------------------- 
    514 \subsubsection[UBS: Upstream Biased Scheme (\forcode{ln_dynadv_ubs = .true.})]{UBS: Upstream Biased Scheme (\protect\np{ln\_dynadv\_ubs}\forcode{ = .true.})} 
     514\subsubsection[UBS: Upstream Biased Scheme (\forcode{ln_dynadv_ubs})]{UBS: Upstream Biased Scheme (\protect\np{ln\_dynadv\_ubs})} 
    515515\label{subsec:DYN_adv_ubs} 
    516516 
    … …  
    591591%           z-coordinate with full step 
    592592%-------------------------------------------------------------------------------------------------------------- 
    593 \subsection[Full step $Z$-coordinate (\forcode{ln_dynhpg_zco = .true.})]{Full step $Z$-coordinate (\protect\np{ln\_dynhpg\_zco}\forcode{ = .true.})} 
     593\subsection[Full step $Z$-coordinate (\forcode{ln_dynhpg_zco})]{Full step $Z$-coordinate (\protect\np{ln\_dynhpg\_zco})} 
    594594\label{subsec:DYN_hpg_zco} 
    595595 
    … …  
    636636%           z-coordinate with partial step 
    637637%-------------------------------------------------------------------------------------------------------------- 
    638 \subsection[Partial step $Z$-coordinate (\forcode{ln_dynhpg_zps = .true.})]{Partial step $Z$-coordinate (\protect\np{ln\_dynhpg\_zps}\forcode{ = .true.})} 
     638\subsection[Partial step $Z$-coordinate (\forcode{ln_dynhpg_zps})]{Partial step $Z$-coordinate (\protect\np{ln\_dynhpg\_zps})} 
    639639\label{subsec:DYN_hpg_zps} 
    640640 
    … …  
    722722%           Time-scheme 
    723723%-------------------------------------------------------------------------------------------------------------- 
    724 \subsection[Time-scheme (\forcode{ln_dynhpg_imp = .{true,false}.})]{Time-scheme (\protect\np{ln\_dynhpg\_imp}\forcode{ = .\{true,false\}}.)} 
     724\subsection[Time-scheme (\forcode{ln_dynhpg_imp})]{Time-scheme (\protect\np{ln\_dynhpg\_imp})} 
    725725\label{subsec:DYN_hpg_imp} 
    726726 
    … …  
    825825% Explicit free surface formulation 
    826826%-------------------------------------------------------------------------------------------------------------- 
    827 \subsection[Explicit free surface (\texttt{ln\_dynspg\_exp}\forcode{ = .true.})]{Explicit free surface (\protect\np{ln\_dynspg\_exp}\forcode{ = .true.})} 
     827\subsection[Explicit free surface (\forcode{ln_dynspg_exp})]{Explicit free surface (\protect\np{ln\_dynspg\_exp})} 
    828828\label{subsec:DYN_spg_exp} 
    829829 
    … …  
    851851% Split-explict free surface formulation 
    852852%-------------------------------------------------------------------------------------------------------------- 
    853 \subsection[Split-explicit free surface (\texttt{ln\_dynspg\_ts}\forcode{ = .true.})]{Split-explicit free surface (\protect\np{ln\_dynspg\_ts}\forcode{ = .true.})} 
     853\subsection[Split-explicit free surface (\forcode{ln_dynspg_ts})]{Split-explicit free surface (\protect\np{ln\_dynspg\_ts})} 
    854854\label{subsec:DYN_spg_ts} 
    855855%------------------------------------------namsplit----------------------------------------------------------- 
    … …  
    10961096% Filtered free surface formulation 
    10971097%-------------------------------------------------------------------------------------------------------------- 
    1098 \subsection[Filtered free surface (\texttt{dynspg\_flt?})]{Filtered free surface (\protect\texttt{dynspg\_flt?})} 
     1098\subsection[Filtered free surface (\forcode{dynspg_flt?})]{Filtered free surface (\protect\texttt{dynspg\_flt?})} 
    10991099\label{subsec:DYN_spg_fltp} 
    11001100 
    … …  
    11621162 
    11631163% ================================================================ 
    1164 \subsection[Iso-level laplacian (\forcode{ln_dynldf_lap = .true.})]{Iso-level laplacian operator (\protect\np{ln\_dynldf\_lap}\forcode{ = .true.})} 
     1164\subsection[Iso-level laplacian (\forcode{ln_dynldf_lap})]{Iso-level laplacian operator (\protect\np{ln\_dynldf\_lap})} 
    11651165\label{subsec:DYN_ldf_lap} 
    11661166 
    … …  
    11871187%           Rotated laplacian operator 
    11881188%-------------------------------------------------------------------------------------------------------------- 
    1189 \subsection[Rotated laplacian (\forcode{ln_dynldf_iso = .true.})]{Rotated laplacian operator (\protect\np{ln\_dynldf\_iso}\forcode{ = .true.})} 
     1189\subsection[Rotated laplacian (\forcode{ln_dynldf_iso})]{Rotated laplacian operator (\protect\np{ln\_dynldf\_iso})} 
    11901190\label{subsec:DYN_ldf_iso} 
    11911191 
    … …  
    12451245%           Iso-level bilaplacian operator 
    12461246%-------------------------------------------------------------------------------------------------------------- 
    1247 \subsection[Iso-level bilaplacian (\forcode{ln_dynldf_bilap = .true.})]{Iso-level bilaplacian operator (\protect\np{ln\_dynldf\_bilap}\forcode{ = .true.})} 
     1247\subsection[Iso-level bilaplacian (\forcode{ln_dynldf_bilap})]{Iso-level bilaplacian operator (\protect\np{ln\_dynldf\_bilap})} 
    12481248\label{subsec:DYN_ldf_bilap} 
    12491249 

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

    r11561 r11565  
    3434% Lateral Mixing Operator 
    3535% ================================================================ 
    36 \section[Lateral mixing operators] 
    37 {Lateral mixing operators} 
     36\section[Lateral mixing operators]{Lateral mixing operators} 
    3837\label{sec:LDF_op} 
    3938We remind here the different lateral mixing operators that can be used. Further details can be found in \autoref{subsec:TRA_ldf_op} and  \autoref{sec:DYN_ldf}. 
    4039 
    41 \subsection[No lateral mixing (\forcode{ln_traldf_OFF}, \forcode{ln_dynldf_OFF})] 
    42 {No lateral mixing (\protect\np{ln\_traldf\_OFF}, \protect\np{ln\_dynldf\_OFF})} 
     40\subsection[No lateral mixing (\forcode{ln_traldf_OFF} \& \forcode{ln_dynldf_OFF})]{No lateral mixing (\protect\np{ln\_traldf\_OFF} \& \protect\np{ln\_dynldf\_OFF})} 
    4341 
    4442It is possible to run without explicit lateral diffusion on tracers (\protect\np{ln\_traldf\_OFF}\forcode{=.true.}) and/or 
    … …  
    4745see \autoref{subsec:DYN_adv_ubs}) and can be useful for testing purposes. 
    4846 
    49 \subsection[Laplacian mixing (\forcode{ln_traldf_lap}, \forcode{ln_dynldf_lap})] 
    50 {Laplacian mixing (\protect\np{ln\_traldf\_lap}, \protect\np{ln\_dynldf\_lap})} 
     47\subsection[Laplacian mixing (\forcode{ln_traldf_lap} \& \forcode{ln_dynldf_lap})]{Laplacian mixing (\protect\np{ln\_traldf\_lap} \& \protect\np{ln\_dynldf\_lap})} 
    5148Setting \protect\np{ln\_traldf\_lap}\forcode{=.true.} and/or \protect\np{ln\_dynldf\_lap}\forcode{=.true.} enables 
    5249a second order diffusion on tracers and momentum respectively. Note that in \NEMO\ 4, one can not combine 
    5350Laplacian and Bilaplacian operators for the same variable. 
    5451 
    55 \subsection[Bilaplacian mixing (\forcode{ln_traldf_blp}, \forcode{ln_dynldf_blp})] 
    56 {Bilaplacian mixing (\protect\np{ln\_traldf\_blp}, \protect\np{ln\_dynldf\_blp})} 
     52\subsection[Bilaplacian mixing (\forcode{ln_traldf_blp} \& \forcode{ln_dynldf_blp})]{Bilaplacian mixing (\protect\np{ln\_traldf\_blp} \& \protect\np{ln\_dynldf\_blp})} 
    5753Setting \protect\np{ln\_traldf\_blp}\forcode{=.true.} and/or \protect\np{ln\_dynldf\_blp}\forcode{=.true.} enables 
    5854a fourth order diffusion on tracers and momentum respectively. It is implemented by calling the above Laplacian operator twice. 
    … …  
    6258% Direction of lateral Mixing 
    6359% ================================================================ 
    64 \section[Direction of lateral mixing (\textit{ldfslp.F90})] 
    65 {Direction of lateral mixing (\protect\mdl{ldfslp})} 
     60\section[Direction of lateral mixing (\textit{ldfslp.F90})]{Direction of lateral mixing (\protect\mdl{ldfslp})} 
    6661\label{sec:LDF_slp} 
    6762 
    … …  
    325320% Lateral Mixing Coefficients 
    326321% ================================================================ 
    327 \section[Lateral mixing coefficient (\forcode{nn_aht_ijk_t}, \forcode{nn_ahm_ijk_t})] 
    328 {Lateral mixing coefficient (\protect\np{nn\_aht\_ijk\_t}, \protect\np{nn\_ahm\_ijk\_t})} 
     322\section[Lateral mixing coefficient (\forcode{nn_aht_ijk_t} \& \forcode{nn_ahm_ijk_t})]{Lateral mixing coefficient (\protect\np{nn\_aht\_ijk\_t} \& \protect\np{nn\_ahm\_ijk\_t})} 
    329323\label{sec:LDF_coef} 
    330324 
    … …  
    332326The way the mixing coefficients are set in the reference version can be described as follows: 
    333327 
    334 \subsection[Mixing coefficients read from file (\forcode{nn_aht_ijk_t=-20, -30}, \forcode{nn_ahm_ijk_t=-20,-30})] 
    335 { Mixing coefficients read from file (\protect\np{nn\_aht\_ijk\_t}\forcode{=-20, -30}, \protect\np{nn\_ahm\_ijk\_t}\forcode{=-20, -30})} 
     328\subsection[Mixing coefficients read from file (\forcode{=-20, -30})]{ Mixing coefficients read from file (\protect\np{nn\_aht\_ijk\_t}\forcode{=-20, -30} \& \protect\np{nn\_ahm\_ijk\_t}\forcode{=-20, -30})} 
    336329 
    337330Mixing coefficients can be read from file if a particular geographical variation is needed. For example, in the ORCA2 global ocean model, 
    … …  
    357350%-------------------------------------------------------------------------------------------------------------- 
    358351 
    359 \subsection[Constant mixing coefficients (\forcode{nn_aht_ijk_t=0}, \forcode{nn_ahm_ijk_t=0})] 
    360 { Constant mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=0}, \protect\np{nn\_ahm\_ijk\_t}\forcode{=0})} 
     352\subsection[Constant mixing coefficients (\forcode{=0})]{ Constant mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=0} \& \protect\np{nn\_ahm\_ijk\_t}\forcode{=0})} 
    361353 
    362354If constant, mixing coefficients are set thanks to a velocity and a length scales ($U_{scl}$, $L_{scl}$) such that: 
    … …  
    374366 $U_{scl}$ and $L_{scl}$ are given by the namelist parameters \np{rn\_Ud}, \np{rn\_Uv}, \np{rn\_Ld} and \np{rn\_Lv}. 
    375367 
    376 \subsection[Vertically varying mixing coefficients (\forcode{nn_aht_ijk_t=10}, \forcode{nn_ahm_ijk_t=10})] 
    377 {Vertically varying mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=10}, \protect\np{nn\_ahm\_ijk\_t}\forcode{=10})} 
     368\subsection[Vertically varying mixing coefficients (\forcode{=10})]{Vertically varying mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=10} \& \protect\np{nn\_ahm\_ijk\_t}\forcode{=10})} 
    378369 
    379370In the vertically varying case, a hyperbolic variation of the lateral mixing coefficient is introduced in which 
    … …  
    382373This profile is hard coded in module \mdl{ldfc1d\_c2d}, but can be easily modified by users. 
    383374 
    384 \subsection[Mesh size dependent mixing coefficients (\forcode{nn_aht_ijk_t=20}, \forcode{nn_ahm_ijk_t=20})] 
    385 {Mesh size dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=20}, \protect\np{nn\_ahm\_ijk\_t}\forcode{=20})} 
     375\subsection[Mesh size dependent mixing coefficients (\forcode{=20})]{Mesh size dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=20} \& \protect\np{nn\_ahm\_ijk\_t}\forcode{=20})} 
    386376 
    387377In that case, the horizontal variation of the eddy coefficient depends on the local mesh size and 
    … …  
    408398\colorbox{yellow}{CASE \np{nn\_aht\_ijk\_t} = 21 to be added} 
    409399 
    410 \subsection[Mesh size and depth dependent mixing coefficients (\forcode{nn_aht_ijk_t=30}, \forcode{nn_ahm_ijk_t=30})] 
    411 {Mesh size and depth dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=30}, \protect\np{nn\_ahm\_ijk\_t}\forcode{=30})} 
     400\subsection[Mesh size and depth dependent mixing coefficients (\forcode{=30})]{Mesh size and depth dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=30} \& \protect\np{nn\_ahm\_ijk\_t}\forcode{=30})} 
    412401 
    413402The 3D space variation of the mixing coefficient is simply the combination of the 1D and 2D cases above, 
    … …  
    415404the magnitude of the coefficient. 
    416405 
    417 \subsection[Velocity dependent mixing coefficients (\forcode{nn_aht_ijk_t=31}, \forcode{nn_ahm_ijk_t=31})] 
    418 {Flow dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=31}, \protect\np{nn\_ahm\_ijk\_t}\forcode{=31})} 
     406\subsection[Velocity dependent mixing coefficients (\forcode{=31})]{Flow dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=31} \& \protect\np{nn\_ahm\_ijk\_t}\forcode{=31})} 
    419407In 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 $12$): 
    420408\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 ?} 
    … …  
    430418\end{equation} 
    431419 
    432 \subsection[Deformation rate dependent viscosities (\forcode{nn_ahm_ijk_t=32})] 
    433 {Deformation rate dependent viscosities (\protect\np{nn\_ahm\_ijk\_t}\forcode{=32})} 
     420\subsection[Deformation rate dependent viscosities (\forcode{nn_ahm_ijk_t=32})]{Deformation rate dependent viscosities (\protect\np{nn\_ahm\_ijk\_t}\forcode{=32})} 
    434421 
    435422This option refers to the \citep{smagorinsky_MW63} scheme which is here implemented for momentum only. Smagorinsky chose as a 
    … …  
    483470% Eddy Induced Mixing 
    484471% ================================================================ 
    485 \section[Eddy induced velocity (\forcode{ln_ldfeiv=.true.})] 
    486 {Eddy induced velocity (\protect\np{ln\_ldfeiv}\forcode{=.true.})} 
     472\section[Eddy induced velocity (\forcode{ln_ldfeiv})]{Eddy induced velocity (\protect\np{ln\_ldfeiv})} 
    487473 
    488474\label{sec:LDF_eiv} 
    … …  
    555541% Mixed layer eddies 
    556542% ================================================================ 
    557 \section[Mixed layer eddies (\forcode{ln_mle=.true.})] 
    558 {Mixed layer eddies (\protect\np{ln\_mle}\forcode{=.true.})} 
    559  
     543\section[Mixed layer eddies (\forcode{ln_mle})]{Mixed layer eddies (\protect\np{ln\_mle})} 
    560544\label{sec:LDF_mle} 
    561545 

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

    r11561 r11565  
    6060% Tracer Advection 
    6161% ================================================================ 
    62 \section[Tracer advection (\textit{traadv.F90})] 
    63 {Tracer advection (\protect\mdl{traadv})} 
     62\section[Tracer advection (\textit{traadv.F90})]{Tracer advection (\protect\mdl{traadv})} 
    6463\label{sec:TRA_adv} 
    6564%------------------------------------------namtra_adv----------------------------------------------------- 
    … …  
    186185%        2nd and 4th order centred schemes 
    187186% ------------------------------------------------------------------------------------------------------------- 
    188 \subsection[CEN: Centred scheme (\forcode{ln_traadv_cen=.true.})] 
    189 {CEN: Centred scheme (\protect\np{ln\_traadv\_cen}\forcode{=.true.})} 
     187\subsection[CEN: Centred scheme (\forcode{ln_traadv_cen})]{CEN: Centred scheme (\protect\np{ln\_traadv\_cen})} 
    190188\label{subsec:TRA_adv_cen} 
    191189 
    … …  
    254252%        FCT scheme 
    255253% ------------------------------------------------------------------------------------------------------------- 
    256 \subsection[FCT: Flux Corrected Transport scheme (\forcode{ln_traadv_fct=.true.})] 
    257 {FCT: Flux Corrected Transport scheme (\protect\np{ln\_traadv\_fct}\forcode{=.true.})} 
     254\subsection[FCT: Flux Corrected Transport scheme (\forcode{ln_traadv_fct})]{FCT: Flux Corrected Transport scheme (\protect\np{ln\_traadv\_fct})} 
    258255\label{subsec:TRA_adv_tvd} 
    259256 
    … …  
    298295%        MUSCL scheme 
    299296% ------------------------------------------------------------------------------------------------------------- 
    300 \subsection[MUSCL: Monotone Upstream Scheme for Conservative Laws (\forcode{ln_traadv_mus=.true.})] 
    301 {MUSCL: Monotone Upstream Scheme for Conservative Laws (\protect\np{ln\_traadv\_mus}\forcode{=.true.})} 
     297\subsection[MUSCL: Monotone Upstream Scheme for Conservative Laws (\forcode{ln_traadv_mus})]{MUSCL: Monotone Upstream Scheme for Conservative Laws (\protect\np{ln\_traadv\_mus})} 
    302298\label{subsec:TRA_adv_mus} 
    303299 
    … …  
    335331%        UBS scheme 
    336332% ------------------------------------------------------------------------------------------------------------- 
    337 \subsection[UBS a.k.a. UP3: Upstream-Biased Scheme (\forcode{ln_traadv_ubs=.true.})] 
    338 {UBS a.k.a. UP3: Upstream-Biased Scheme (\protect\np{ln\_traadv\_ubs}\forcode{=.true.})} 
     333\subsection[UBS a.k.a. UP3: Upstream-Biased Scheme (\forcode{ln_traadv_ubs})]{UBS a.k.a. UP3: Upstream-Biased Scheme (\protect\np{ln\_traadv\_ubs})} 
    339334\label{subsec:TRA_adv_ubs} 
    340335 
    … …  
    408403%        QCK scheme 
    409404% ------------------------------------------------------------------------------------------------------------- 
    410 \subsection[QCK: QuiCKest scheme (\forcode{ln_traadv_qck=.true.})] 
    411 {QCK: QuiCKest scheme (\protect\np{ln\_traadv\_qck}\forcode{=.true.})} 
     405\subsection[QCK: QuiCKest scheme (\forcode{ln_traadv_qck})]{QCK: QuiCKest scheme (\protect\np{ln\_traadv\_qck})} 
    412406\label{subsec:TRA_adv_qck} 
    413407 
    … …  
    432426% Tracer Lateral Diffusion 
    433427% ================================================================ 
    434 \section[Tracer lateral diffusion (\textit{traldf.F90})] 
    435 {Tracer lateral diffusion (\protect\mdl{traldf})} 
     428\section[Tracer lateral diffusion (\textit{traldf.F90})]{Tracer lateral diffusion (\protect\mdl{traldf})} 
    436429\label{sec:TRA_ldf} 
    437430%-----------------------------------------nam_traldf------------------------------------------------------ 
    … …  
    465458%        Type of operator 
    466459% ------------------------------------------------------------------------------------------------------------- 
    467 \subsection[Type of operator (\texttt{ln\_traldf}\{\texttt{\_OFF,\_lap,\_blp}\})] 
    468 {Type of operator (\protect\np{ln\_traldf\_OFF}, \protect\np{ln\_traldf\_lap}, or \protect\np{ln\_traldf\_blp}) } 
     460\subsection[Type of operator (\texttt{ln\_traldf}\{\texttt{\_OFF,\_lap,\_blp}\})]{Type of operator (\protect\np{ln\_traldf\_OFF}, \protect\np{ln\_traldf\_lap}, or \protect\np{ln\_traldf\_blp})} 
    469461\label{subsec:TRA_ldf_op} 
    470462 
    … …  
    500492%        Direction of action 
    501493% ------------------------------------------------------------------------------------------------------------- 
    502 \subsection[Action direction (\texttt{ln\_traldf}\{\texttt{\_lev,\_hor,\_iso,\_triad}\})] 
    503 {Direction of action (\protect\np{ln\_traldf\_lev}, \protect\np{ln\_traldf\_hor}, \protect\np{ln\_traldf\_iso}, or \protect\np{ln\_traldf\_triad}) } 
     494\subsection[Action direction (\texttt{ln\_traldf}\{\texttt{\_lev,\_hor,\_iso,\_triad}\})]{Direction of action (\protect\np{ln\_traldf\_lev}, \protect\np{ln\_traldf\_hor}, \protect\np{ln\_traldf\_iso}, or \protect\np{ln\_traldf\_triad})} 
    504495\label{subsec:TRA_ldf_dir} 
    505496 
    … …  
    527518%       iso-level operator 
    528519% ------------------------------------------------------------------------------------------------------------- 
    529 \subsection[Iso-level (bi-)laplacian operator (\texttt{ln\_traldf\_iso})] 
    530 {Iso-level (bi-)laplacian operator ( \protect\np{ln\_traldf\_iso})} 
     520\subsection[Iso-level (bi-)laplacian operator (\texttt{ln\_traldf\_iso})]{Iso-level (bi-)laplacian operator ( \protect\np{ln\_traldf\_iso})} 
    531521\label{subsec:TRA_ldf_lev} 
    532522 
    … …  
    564554%&&    Standard rotated (bi-)laplacian operator 
    565555%&& ---------------------------------------------- 
    566 \subsubsection[Standard rotated (bi-)laplacian operator (\textit{traldf\_iso.F90})] 
    567 {Standard rotated (bi-)laplacian operator (\protect\mdl{traldf\_iso})} 
     556\subsubsection[Standard rotated (bi-)laplacian operator (\textit{traldf\_iso.F90})]{Standard rotated (bi-)laplacian operator (\protect\mdl{traldf\_iso})} 
    568557\label{subsec:TRA_ldf_iso} 
    569558The general form of the second order lateral tracer subgrid scale physics (\autoref{eq:MB_zdf}) 
    … …  
    608597%&&     Triad rotated (bi-)laplacian operator 
    609598%&&  ------------------------------------------- 
    610 \subsubsection[Triad rotated (bi-)laplacian operator (\textit{ln\_traldf\_triad})] 
    611 {Triad rotated (bi-)laplacian operator (\protect\np{ln\_traldf\_triad})} 
     599\subsubsection[Triad rotated (bi-)laplacian operator (\textit{ln\_traldf\_triad})]{Triad rotated (bi-)laplacian operator (\protect\np{ln\_traldf\_triad})} 
    612600\label{subsec:TRA_ldf_triad} 
    613601 
    … …  
    641629% Tracer Vertical Diffusion 
    642630% ================================================================ 
    643 \section[Tracer vertical diffusion (\textit{trazdf.F90})] 
    644 {Tracer vertical diffusion (\protect\mdl{trazdf})} 
     631\section[Tracer vertical diffusion (\textit{trazdf.F90})]{Tracer vertical diffusion (\protect\mdl{trazdf})} 
    645632\label{sec:TRA_zdf} 
    646633%--------------------------------------------namzdf--------------------------------------------------------- 
    … …  
    685672%        surface boundary condition 
    686673% ------------------------------------------------------------------------------------------------------------- 
    687 \subsection[Surface boundary condition (\textit{trasbc.F90})] 
    688 {Surface boundary condition (\protect\mdl{trasbc})} 
     674\subsection[Surface boundary condition (\textit{trasbc.F90})]{Surface boundary condition (\protect\mdl{trasbc})} 
    689675\label{subsec:TRA_sbc} 
    690676 
    … …  
    759745%        Solar Radiation Penetration 
    760746% ------------------------------------------------------------------------------------------------------------- 
    761 \subsection[Solar radiation penetration (\textit{traqsr.F90})] 
    762 {Solar radiation penetration (\protect\mdl{traqsr})} 
     747\subsection[Solar radiation penetration (\textit{traqsr.F90})]{Solar radiation penetration (\protect\mdl{traqsr})} 
    763748\label{subsec:TRA_qsr} 
    764749%--------------------------------------------namqsr-------------------------------------------------------- 
    … …  
    883868%        Bottom Boundary Condition 
    884869% ------------------------------------------------------------------------------------------------------------- 
    885 \subsection[Bottom boundary condition (\textit{trabbc.F90}) - \forcode{ln_trabbc=.true.})] 
    886 {Bottom boundary condition (\protect\mdl{trabbc})} 
     870\subsection[Bottom boundary condition (\textit{trabbc.F90}) - \forcode{ln_trabbc})]{Bottom boundary condition (\protect\mdl{trabbc} - \protect\np{ln\_trabbc})} 
    887871\label{subsec:TRA_bbc} 
    888872%--------------------------------------------nambbc-------------------------------------------------------- 
    … …  
    924908% Bottom Boundary Layer 
    925909% ================================================================ 
    926 \section[Bottom boundary layer (\textit{trabbl.F90} - \forcode{ln_trabbl=.true.})] 
    927 {Bottom boundary layer (\protect\mdl{trabbl} - \protect\np{ln\_trabbl}\forcode{=.true.})} 
     910\section[Bottom boundary layer (\textit{trabbl.F90} - \forcode{ln_trabbl})]{Bottom boundary layer (\protect\mdl{trabbl} - \protect\np{ln\_trabbl})} 
    928911\label{sec:TRA_bbl} 
    929912%--------------------------------------------nambbl--------------------------------------------------------- 
    … …  
    961944%        Diffusive BBL 
    962945% ------------------------------------------------------------------------------------------------------------- 
    963 \subsection[Diffusive bottom boundary layer (\forcode{nn_bbl_ldf=1})] 
    964 {Diffusive bottom boundary layer (\protect\np{nn\_bbl\_ldf}\forcode{=1})} 
     946\subsection[Diffusive bottom boundary layer (\forcode{nn_bbl_ldf=1})]{Diffusive bottom boundary layer (\protect\np{nn\_bbl\_ldf}\forcode{=1})} 
    965947\label{subsec:TRA_bbl_diff} 
    966948 
    … …  
    1001983%        Advective BBL 
    1002984% ------------------------------------------------------------------------------------------------------------- 
    1003 \subsection[Advective bottom boundary layer (\forcode{nn_bbl_adv=[12]})] 
    1004 {Advective bottom boundary layer (\protect\np{nn\_bbl\_adv}\forcode{=[12]})} 
     985\subsection[Advective bottom boundary layer (\forcode{nn_bbl_adv=[12]})]{Advective bottom boundary layer (\protect\np{nn\_bbl\_adv}\forcode{=[12]})} 
    1005986\label{subsec:TRA_bbl_adv} 
    1006987 
    … …  
    10931074% Tracer damping 
    10941075% ================================================================ 
    1095 \section[Tracer damping (\textit{tradmp.F90})] 
    1096 {Tracer damping (\protect\mdl{tradmp})} 
     1076\section[Tracer damping (\textit{tradmp.F90})]{Tracer damping (\protect\mdl{tradmp})} 
    10971077\label{sec:TRA_dmp} 
    10981078%--------------------------------------------namtra_dmp------------------------------------------------- 
    … …  
    11531133% Tracer time evolution 
    11541134% ================================================================ 
    1155 \section[Tracer time evolution (\textit{tranxt.F90})] 
    1156 {Tracer time evolution (\protect\mdl{tranxt})} 
     1135\section[Tracer time evolution (\textit{tranxt.F90})]{Tracer time evolution (\protect\mdl{tranxt})} 
    11571136\label{sec:TRA_nxt} 
    11581137%--------------------------------------------namdom----------------------------------------------------- 
    … …  
    11891168% Equation of State (eosbn2) 
    11901169% ================================================================ 
    1191 \section[Equation of state (\textit{eosbn2.F90})] 
    1192 {Equation of state (\protect\mdl{eosbn2})} 
     1170\section[Equation of state (\textit{eosbn2.F90})]{Equation of state (\protect\mdl{eosbn2})} 
    11931171\label{sec:TRA_eosbn2} 
    11941172%--------------------------------------------nameos----------------------------------------------------- 
    … …  
    12041182%        Equation of State 
    12051183% ------------------------------------------------------------------------------------------------------------- 
    1206 \subsection[Equation of seawater (\texttt{ln}\{\texttt{\_teso10,\_eos80,\_seos}\})] 
    1207 {Equation of seawater (\protect\np{ln\_teos10}, \protect\np{ln\_teos80}, or \protect\np{ln\_seos}) } 
     1184\subsection[Equation of seawater (\texttt{ln}\{\texttt{\_teso10,\_eos80,\_seos}\})]{Equation of seawater (\protect\np{ln\_teos10}, \protect\np{ln\_teos80}, or \protect\np{ln\_seos})} 
    12081185\label{subsec:TRA_eos} 
    12091186 
    … …  
    13301307%        Brunt-V\"{a}is\"{a}l\"{a} Frequency 
    13311308% ------------------------------------------------------------------------------------------------------------- 
    1332 \subsection[Brunt-V\"{a}is\"{a}l\"{a} frequency] 
    1333 {Brunt-V\"{a}is\"{a}l\"{a} frequency} 
     1309\subsection[Brunt-V\"{a}is\"{a}l\"{a} frequency]{Brunt-V\"{a}is\"{a}l\"{a} frequency} 
    13341310\label{subsec:TRA_bn2} 
    13351311 
    … …  
    13851361% Horizontal Derivative in zps-coordinate 
    13861362% ================================================================ 
    1387 \section[Horizontal derivative in \textit{zps}-coordinate (\textit{zpshde.F90})] 
    1388 {Horizontal derivative in \textit{zps}-coordinate (\protect\mdl{zpshde})} 
     1363\section[Horizontal derivative in \textit{zps}-coordinate (\textit{zpshde.F90})]{Horizontal derivative in \textit{zps}-coordinate (\protect\mdl{zpshde})} 
    13891364\label{sec:TRA_zpshde} 
    13901365 

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

    r11561 r11565  
    5858%        Constant 
    5959% ------------------------------------------------------------------------------------------------------------- 
    60 \subsection[Constant (\forcode{ln_zdfcst=.true.})] 
    61 {Constant (\protect\np{ln\_zdfcst}\forcode{=.true.})} 
     60\subsection[Constant (\forcode{ln_zdfcst})]{Constant (\protect\np{ln\_zdfcst})} 
    6261\label{subsec:ZDF_cst} 
    6362 
    … …  
    8180%        Richardson Number Dependent 
    8281% ------------------------------------------------------------------------------------------------------------- 
    83 \subsection[Richardson number dependent (\forcode{ln_zdfric=.true.})] 
    84 {Richardson number dependent (\protect\np{ln\_zdfric}\forcode{=.true.})} 
     82\subsection[Richardson number dependent (\forcode{ln_zdfric})]{Richardson number dependent (\protect\np{ln\_zdfric})} 
    8583\label{subsec:ZDF_ric} 
    8684 
    … …  
    143141%        TKE Turbulent Closure Scheme 
    144142% ------------------------------------------------------------------------------------------------------------- 
    145 \subsection[TKE turbulent closure scheme (\forcode{ln_zdftke=.true.})] 
    146 {TKE turbulent closure scheme (\protect\np{ln\_zdftke}\forcode{=.true.})} 
     143\subsection[TKE turbulent closure scheme (\forcode{ln_zdftke})]{TKE turbulent closure scheme (\protect\np{ln\_zdftke})} 
    147144\label{subsec:ZDF_tke} 
    148145%--------------------------------------------namzdf_tke-------------------------------------------------- 
    … …  
    427424%        GLS Generic Length Scale Scheme 
    428425% ------------------------------------------------------------------------------------------------------------- 
    429 \subsection[GLS: Generic Length Scale (\forcode{ln_zdfgls=.true.})] 
    430 {GLS: Generic Length Scale (\protect\np{ln\_zdfgls}\forcode{=.true.})} 
     426\subsection[GLS: Generic Length Scale (\forcode{ln_zdfgls})]{GLS: Generic Length Scale (\protect\np{ln\_zdfgls})} 
    431427\label{subsec:ZDF_gls} 
    432428 
    … …  
    552548%        OSM OSMOSIS BL Scheme 
    553549% ------------------------------------------------------------------------------------------------------------- 
    554 \subsection[OSM: OSMosis boundary layer scheme (\forcode{ln_zdfosm=.true.})] 
    555 {OSM: OSMosis boundary layer scheme (\protect\np{ln\_zdfosm}\forcode{=.true.})} 
     550\subsection[OSM: OSMosis boundary layer scheme (\forcode{ln_zdfosm})]{OSM: OSMosis boundary layer scheme (\protect\np{ln\_zdfosm})} 
    556551\label{subsec:ZDF_osm} 
    557552%--------------------------------------------namzdf_osm--------------------------------------------------------- 
    … …  
    569564%        TKE and GLS discretization considerations 
    570565% ------------------------------------------------------------------------------------------------------------- 
    571 \subsection[ Discrete energy conservation for TKE and GLS schemes] 
    572 {Discrete energy conservation for TKE and GLS schemes} 
     566\subsection[ Discrete energy conservation for TKE and GLS schemes]{Discrete energy conservation for TKE and GLS schemes} 
    573567\label{subsec:ZDF_tke_ene} 
    574568 
    … …  
    688682%       Non-Penetrative Convective Adjustment 
    689683% ------------------------------------------------------------------------------------------------------------- 
    690 \subsection[Non-penetrative convective adjustment (\forcode{ln_tranpc=.true.})] 
    691 {Non-penetrative convective adjustment (\protect\np{ln\_tranpc}\forcode{=.true.})} 
     684\subsection[Non-penetrative convective adjustment (\forcode{ln_tranpc})]{Non-penetrative convective adjustment (\protect\np{ln\_tranpc})} 
    692685\label{subsec:ZDF_npc} 
    693686 
    … …  
    754747%       Enhanced Vertical Diffusion 
    755748% ------------------------------------------------------------------------------------------------------------- 
    756 \subsection[Enhanced vertical diffusion (\forcode{ln_zdfevd=.true.})] 
    757 {Enhanced vertical diffusion (\protect\np{ln\_zdfevd}\forcode{=.true.})} 
     749\subsection[Enhanced vertical diffusion (\forcode{ln_zdfevd})]{Enhanced vertical diffusion (\protect\np{ln\_zdfevd})} 
    758750\label{subsec:ZDF_evd} 
    759751 
    … …  
    781773%       Turbulent Closure Scheme 
    782774% ------------------------------------------------------------------------------------------------------------- 
    783 \subsection{Handling convection with turbulent closure schemes (\forcode{ln_zdf{tke,gls,osm}=.true.})} 
     775\subsection[Handling convection with turbulent closure schemes (\forcode{ln_zdf{tke,gls,osm}})]{Handling convection with turbulent closure schemes (\forcode{ln_zdf{tke,gls,osm}})} 
    784776\label{subsec:ZDF_tcs} 
    785777 
    … …  
    809801% Double Diffusion Mixing 
    810802% ================================================================ 
    811 \section[Double diffusion mixing (\forcode{ln_zdfddm=.true.})] 
    812 {Double diffusion mixing (\protect\np{ln\_zdfddm}\forcode{=.true.})} 
     803\section[Double diffusion mixing (\forcode{ln_zdfddm})]{Double diffusion mixing (\protect\np{ln\_zdfddm})} 
    813804\label{subsec:ZDF_ddm} 
    814805 
    … …  
    905896% Bottom Friction 
    906897% ================================================================ 
    907  \section[Bottom and top friction (\textit{zdfdrg.F90})] 
    908  {Bottom and top friction (\protect\mdl{zdfdrg})} 
    909  \label{sec:ZDF_drg} 
     898\section[Bottom and top friction (\textit{zdfdrg.F90})] {Bottom and top friction (\protect\mdl{zdfdrg})} 
     899\label{sec:ZDF_drg} 
    910900 
    911901%--------------------------------------------namdrg-------------------------------------------------------- 
    … …  
    986976%       Linear Bottom Friction 
    987977% ------------------------------------------------------------------------------------------------------------- 
    988  \subsection[Linear top/bottom friction (\forcode{ln_lin=.true.})] 
    989  {Linear top/bottom friction (\protect\np{ln\_lin}\forcode{=.true.)}} 
    990  \label{subsec:ZDF_drg_linear} 
     978\subsection[Linear top/bottom friction (\forcode{ln_lin})]{Linear top/bottom friction (\protect\np{ln\_lin})} 
     979\label{subsec:ZDF_drg_linear} 
    991980 
    992981The linear friction parameterisation (including the special case of a free-slip condition) assumes that 
    … …  
    10261015%       Non-Linear Bottom Friction 
    10271016% ------------------------------------------------------------------------------------------------------------- 
    1028  \subsection[Non-linear top/bottom friction (\forcode{ln_non_lin=.true.})] 
    1029  {Non-linear top/bottom friction (\protect\np{ln\_non\_lin}\forcode{=.true.})} 
    1030  \label{subsec:ZDF_drg_nonlinear} 
     1017\subsection[Non-linear top/bottom friction (\forcode{ln_non_lin})]{Non-linear top/bottom friction (\protect\np{ln\_non\_lin})} 
     1018\label{subsec:ZDF_drg_nonlinear} 
    10311019 
    10321020The non-linear bottom friction parameterisation assumes that the top/bottom friction is quadratic: 
    … …  
    10621050%       Bottom Friction Log-layer 
    10631051% ------------------------------------------------------------------------------------------------------------- 
    1064  \subsection[Log-layer top/bottom friction (\forcode{ln_loglayer=.true.})] 
    1065  {Log-layer top/bottom friction (\protect\np{ln\_loglayer}\forcode{=.true.})} 
    1066  \label{subsec:ZDF_drg_loglayer} 
     1052\subsection[Log-layer top/bottom friction (\forcode{ln_loglayer})]{Log-layer top/bottom friction (\protect\np{ln\_loglayer})} 
     1053\label{subsec:ZDF_drg_loglayer} 
    10671054 
    10681055In the non-linear friction case, the drag coefficient, $C_D$, can be optionally enhanced using 
    … …  
    10891076%       Explicit bottom Friction 
    10901077% ------------------------------------------------------------------------------------------------------------- 
    1091  \subsection{Explicit top/bottom friction (\forcode{ln_drgimp=.false.})} 
    1092  \label{subsec:ZDF_drg_stability} 
     1078\subsection[Explicit top/bottom friction (\forcode{ln_drgimp=.false.})]{Explicit top/bottom friction (\protect\np{ln\_drgimp}\forcode{=.false.})} 
     1079\label{subsec:ZDF_drg_stability} 
    10931080 
    10941081Setting \np{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: 
    … …  
    11501137%       Implicit Bottom Friction 
    11511138% ------------------------------------------------------------------------------------------------------------- 
    1152  \subsection[Implicit top/bottom friction (\forcode{ln_drgimp=.true.})] 
    1153  {Implicit top/bottom friction (\protect\np{ln\_drgimp}\forcode{=.true.})} 
    1154  \label{subsec:ZDF_drg_imp} 
     1139\subsection[Implicit top/bottom friction (\forcode{ln_drgimp=.true.})]{Implicit top/bottom friction (\protect\np{ln\_drgimp}\forcode{=.true.})} 
     1140\label{subsec:ZDF_drg_imp} 
    11551141 
    11561142An optional implicit form of bottom friction has been implemented to improve model stability. 
    … …  
    11811167%       Bottom Friction with split-explicit free surface 
    11821168% ------------------------------------------------------------------------------------------------------------- 
    1183  \subsection[Bottom friction with split-explicit free surface] 
    1184  {Bottom friction with split-explicit free surface} 
    1185  \label{subsec:ZDF_drg_ts} 
     1169\subsection[Bottom friction with split-explicit free surface]{Bottom friction with split-explicit free surface} 
     1170\label{subsec:ZDF_drg_ts} 
    11861171 
    11871172With 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}\forcode{= .false.} and a centred or \textit{leap-frog} like integration of barotropic equations is used (\ie\ \forcode{ln_bt_fw=.false.}, cf \autoref{subsec:DYN_spg_ts}), this does ensure that barotropic and baroclinic dynamics feel the same stresses during one leapfrog time step. However, if \np{ln\_drgimp}\forcode{= .true.},  stresses depend on the \textit{after} value of the velocities which themselves depend on the barotropic iteration result. This cyclic dependency makes difficult obtaining consistent stresses in 2d and 3d dynamics. Part of this mismatch is then removed when setting the final barotropic component of 3d velocities to the time splitting estimate. This last step can be seen as a necessary evil but should be minimized since it interferes with the adjustment to the boundary conditions. 
    … …  
    11991184% Internal wave-driven mixing 
    12001185% ================================================================ 
    1201 \section[Internal wave-driven mixing (\forcode{ln_zdfiwm=.true.})] 
    1202 {Internal wave-driven mixing (\protect\np{ln\_zdfiwm}\forcode{=.true.})} 
     1186\section[Internal wave-driven mixing (\forcode{ln_zdfiwm})]{Internal wave-driven mixing (\protect\np{ln\_zdfiwm})} 
    12031187\label{subsec:ZDF_tmx_new} 
    12041188 
    … …  
    12641248% surface wave-induced mixing 
    12651249% ================================================================ 
    1266 \section[Surface wave-induced mixing (\forcode{ln_zdfswm=.true.})] 
    1267 {Surface wave-induced mixing (\protect\np{ln\_zdfswm}\forcode{=.true.})} 
     1250\section[Surface wave-induced mixing (\forcode{ln_zdfswm})]{Surface wave-induced mixing (\protect\np{ln\_zdfswm})} 
    12681251\label{subsec:ZDF_swm} 
    12691252 
    … …  
    12981281% Adaptive-implicit vertical advection 
    12991282% ================================================================ 
    1300 \section[Adaptive-implicit vertical advection (\forcode{ln_zad_Aimp=.true.})] 
    1301 {Adaptive-implicit vertical advection(\protect\np{ln\_zad\_Aimp}\forcode{=.true.})} 
     1283\section[Adaptive-implicit vertical advection (\forcode{ln_zad_Aimp})]{Adaptive-implicit vertical advection(\protect\np{ln\_zad\_Aimp})} 
    13021284\label{subsec:ZDF_aimp} 
    13031285 
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