Changeset 11459


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Timestamp:
2019-08-20T10:59:40+02:00 (13 months ago)
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cetlod
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Revision in chapter TRA : mainly removal obsolete CPP keys and update of namelist parameter

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1 edited

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

    r11435 r11459  
    4848associated modules \mdl{eosbn2} and \mdl{phycst}). 
    4949 
    50 The different options available to the user are managed by namelist logicals or CPP keys. 
     50The different options available to the user are managed by namelist logicals. 
    5151For each equation term \textit{TTT}, the namelist logicals are \textit{ln\_traTTT\_xxx}, 
    5252where \textit{xxx} is a 3 or 4 letter acronym corresponding to each optional scheme. 
    53 %The CPP key (when it exists) is \key{traTTT}. 
    5453The equivalent code can be found in the \textit{traTTT} or \textit{traTTT\_xxx} module, 
    5554in the \path{./src/OCE/TRA} directory. 
     
    6968%------------------------------------------------------------------------------------------------------------- 
    7069 
    71 When considered (\ie\ when \np{ln\_traadv\_NONE} is not set to \forcode{.true.}), 
     70When considered (\ie\ when \np{ln\_traadv\_OFF} is not set to \forcode{.true.}), 
    7271the advection tendency of a tracer is expressed in flux form, 
    7372\ie\ as the divergence of the advective fluxes. 
     
    140139two quantities that are not correlated \citep{roullet.madec_JGR00, griffies.pacanowski.ea_MWR01, campin.adcroft.ea_OM04}. 
    141140 
    142 The velocity field that appears in (\autoref{eq:tra_adv} and \autoref{eq:tra_adv_zco?}) is 
     141The velocity field that appears in (\autoref{eq:tra_adv} is  
    143142the centred (\textit{now}) \textit{effective} ocean velocity, \ie\ the \textit{eulerian} velocity 
    144143(see \autoref{chap:DYN}) plus the eddy induced velocity (\textit{eiv}) and/or 
     
    287286A comparison of FCT-2 with MUSCL and a MPDATA scheme can be found in \citet{levy.estublier.ea_GRL01}. 
    288287 
    289 An additional option has been added controlled by \np{nn\_fct\_zts}. 
    290 By setting this integer to a value larger than zero, 
    291 a $2^{nd}$ order FCT scheme is used on both horizontal and vertical direction, but on the latter, 
    292 a split-explicit time stepping is used, with a number of sub-timestep equals to \np{nn\_fct\_zts}. 
    293 This option can be useful when the size of the timestep is limited by vertical advection \citep{lemarie.debreu.ea_OM15}. 
    294 Note that in this case, a similar split-explicit time stepping should be used on vertical advection of momentum to 
    295 insure a better stability (see \autoref{subsec:DYN_zad}). 
    296288 
    297289For stability reasons (see \autoref{chap:STP}), 
     
    375367\citep{shchepetkin.mcwilliams_OM05, demange_phd14}. 
    376368Therefore the vertical flux is evaluated using either a $2^nd$ order FCT scheme or a $4^th$ order COMPACT scheme 
    377 (\np{nn\_cen\_v}\forcode{ = 2 or 4}). 
     369(\np{nn\_ubs\_v}\forcode{ = 2 or 4}). 
    378370 
    379371For stability reasons (see \autoref{chap:STP}), the first term  in \autoref{eq:tra_adv_ubs} 
     
    467459%        Type of operator 
    468460% ------------------------------------------------------------------------------------------------------------- 
    469 \subsection[Type of operator (\texttt{ln\_traldf}\{\texttt{\_NONE,\_lap,\_blp}\})] 
    470 {Type of operator (\protect\np{ln\_traldf\_NONE}, \protect\np{ln\_traldf\_lap}, or \protect\np{ln\_traldf\_blp}) } 
     461\subsection[Type of operator (\texttt{ln\_traldf}\{\texttt{\_OFF,\_lap,\_blp}\})] 
     462{Type of operator (\protect\np{ln\_traldf\_OFF}, \protect\np{ln\_traldf\_lap}, or \protect\np{ln\_traldf\_blp}) } 
    471463\label{subsec:TRA_ldf_op} 
    472464 
     
    474466 
    475467\begin{description} 
    476 \item[\np{ln\_traldf\_NONE}\forcode{ = .true.}:] 
     468\item[\np{ln\_traldf\_OFF}\forcode{ = .true.}:] 
    477469  no operator selected, the lateral diffusive tendency will not be applied to the tracer equation. 
    478470  This option can be used when the selected advection scheme is diffusive enough (MUSCL scheme for example). 
     
    542534where zero diffusive fluxes is assumed across solid boundaries, 
    543535first (and third in bilaplacian case) horizontal tracer derivative are masked. 
    544 It is implemented in the \rou{traldf\_lap} subroutine found in the \mdl{traldf\_lap} module. 
    545 The module also contains \rou{traldf\_blp}, the subroutine calling twice \rou{traldf\_lap} in order to 
     536It is implemented in the \rou{tra\_ldf\_lap} subroutine found in the \mdl{traldf\_lap\_blp}} module. 
     537The module also contains \rou{tra\_ldf\_blp}, the subroutine calling twice \rou{tra\_ldf\_lap} in order to 
    546538compute the iso-level bilaplacian operator. 
    547539 
    548 It is a \textit{horizontal} operator (\ie\ acting along geopotential surfaces) in 
     540It is a \textit{horizontal} operator (\ie acting along geopotential surfaces) in 
    549541the $z$-coordinate with or without partial steps, but is simply an iso-level operator in the $s$-coordinate. 
    550542It is thus used when, in addition to \np{ln\_traldf\_lap} or \np{ln\_traldf\_blp}\forcode{ = .true.}, 
     
    614606\label{subsec:TRA_ldf_triad} 
    615607 
    616 If the Griffies triad scheme is employed (\np{ln\_traldf\_triad}\forcode{ = .true.}; see \autoref{apdx:triad}) 
    617  
    618608An alternative scheme developed by \cite{griffies.gnanadesikan.ea_JPO98} which ensures tracer variance decreases 
    619 is also available in \NEMO\ (\np{ln\_traldf\_grif}\forcode{ = .true.}). 
     609is also available in \NEMO\ (\np{ln\_traldf\_triad}\forcode{ = .true.}). 
    620610A complete description of the algorithm is given in \autoref{apdx:triad}. 
    621611 
     
    665655respectively. 
    666656Generally, $A_w^{vT} = A_w^{vS}$ except when double diffusive mixing is parameterised 
    667 (\ie\ \texttt{zdfddm?} is defined). 
     657(\ie\ \np{ln\_zdfddm} equals \forcode{.true.},). 
    668658The way these coefficients are evaluated is given in \autoref{chap:ZDF} (ZDF). 
    669659Furthermore, when iso-neutral mixing is used, both mixing coefficients are increased by 
     
    677667 
    678668The large eddy coefficient found in the mixed layer together with high vertical resolution implies that 
    679 in the case of explicit time stepping (\np{ln\_zdfexp}\forcode{ = .true.}) 
    680 there would be too restrictive a constraint on the time step. 
    681 Therefore, the default implicit time stepping is preferred for the vertical diffusion since 
     669there would be too restrictive constraint on the time step if we use explicit time stepping. 
     670Therefore an implicit time stepping is preferred for the vertical diffusion since 
    682671it overcomes the stability constraint. 
    683 A forward time differencing scheme (\np{ln\_zdfexp}\forcode{ = .true.}) using 
    684 a time splitting technique (\np{nn\_zdfexp} $> 1$) is provided as an alternative. 
    685 Namelist variables \np{ln\_zdfexp} and \np{nn\_zdfexp} apply to both tracers and dynamics. 
    686672 
    687673% ================================================================ 
     
    777763 
    778764Options are defined through the \nam{tra\_qsr} namelist variables. 
    779 When the penetrative solar radiation option is used (\np{ln\_flxqsr}\forcode{ = .true.}), 
     765When the penetrative solar radiation option is used (\np{ln\_traqsr}\forcode{ = .true.}), 
    780766the solar radiation penetrates the top few tens of meters of the ocean. 
    781 If it is not used (\np{ln\_flxqsr}\forcode{ = .false.}) all the heat flux is absorbed in the first ocean level. 
     767If it is not used (\np{ln\_traqsr}\forcode{ = .false.}) all the heat flux is absorbed in the first ocean level. 
    782768Thus, in the former case a term is added to the time evolution equation of temperature \autoref{eq:PE_tra_T} and 
    783769the surface boundary condition is modified to take into account only the non-penetrative part of the surface 
     
    843829 
    844830\begin{description} 
    845 \item[\np{nn\_chdta}\forcode{ = 0}] 
     831\item[\np{nn\_chldta}\forcode{ = 0}] 
    846832  a constant 0.05 g.Chl/L value everywhere ; 
    847 \item[\np{nn\_chdta}\forcode{ = 1}] 
     833\item[\np{nn\_chldta}\forcode{ = 1}] 
    848834  an observed time varying chlorophyll deduced from satellite surface ocean color measurement spread uniformly in 
    849835  the vertical direction; 
    850 \item[\np{nn\_chdta}\forcode{ = 2}] 
     836\item[\np{nn\_chldta}\forcode{ = 2}] 
    851837  same as previous case except that a vertical profile of chlorophyl is used. 
    852838  Following \cite{morel.berthon_LO89}, the profile is computed from the local surface chlorophyll value; 
     
    854840  simulated time varying chlorophyll by TOP biogeochemical model. 
    855841  In this case, the RGB formulation is used to calculate both the phytoplankton light limitation in 
    856   PISCES or LOBSTER and the oceanic heating rate. 
     842  PISCES and the oceanic heating rate. 
    857843\end{description} 
    858844 
     
    890876%        Bottom Boundary Condition 
    891877% ------------------------------------------------------------------------------------------------------------- 
    892 \subsection[Bottom boundary condition (\textit{trabbc.F90})] 
     878\subsection[Bottom boundary condition (\textit{trabbc.F90}) - \forcode{ln_trabbc = .true.})] 
    893879{Bottom boundary condition (\protect\mdl{trabbc})} 
    894880\label{subsec:TRA_bbc} 
     
    919905(\ie\ the one associated with the Antarctic Bottom Water) by a few Sverdrups \citep{emile-geay.madec_OS09}. 
    920906 
    921 Options are defined through the \nam{tra\_bbc} namelist variables. 
     907Options are defined through the \nam{bbc} namelist variables. 
    922908The presence of geothermal heating is controlled by setting the namelist parameter \np{ln\_trabbc} to true. 
    923909Then, when \np{nn\_geoflx} is set to 1, a constant geothermal heating is introduced whose value is given by 
    924 the \np{nn\_geoflx\_cst}, which is also a namelist parameter. 
     910the \np{rn\_geoflx\_cst}, which is also a namelist parameter. 
    925911When \np{nn\_geoflx} is set to 2, a spatially varying geothermal heat flux is introduced which is provided in 
    926912the \ifile{geothermal\_heating} NetCDF file (\autoref{fig:geothermal}) \citep{emile-geay.madec_OS09}. 
     
    11141100Options are defined through the  \nam{tra\_dmp} namelist variables. 
    11151101The restoring term is added when the namelist parameter \np{ln\_tradmp} is set to true. 
    1116 It also requires that both \np{ln\_tsd\_init} and \np{ln\_tsd\_tradmp} are set to true in 
     1102It also requires that both \np{ln\_tsd\_init} and \np{ln\_tsd\_dmp} are set to true in 
    11171103\nam{tsd} namelist as well as \np{sn\_tem} and \np{sn\_sal} structures are correctly set 
    11181104(\ie\ that $T_o$ and $S_o$ are provided in input files and read using \mdl{fldread}, 
     
    11751161Its default value is \np{rn\_atfp}\forcode{ = 10.e-3}. 
    11761162Note that the forcing correction term in the filter is not applied in linear free surface 
    1177 (\jp{lk\_vvl}\forcode{ = .false.}) (see \autoref{subsec:TRA_sbc}). 
     1163(\jp{ln\_linssh}\forcode{ = .true.}) (see \autoref{subsec:TRA_sbc}). 
    11781164Not also that in constant volume case, the time stepping is performed on $T$, not on its content, $e_{3t}T$. 
    11791165 
     
    11991185%        Equation of State 
    12001186% ------------------------------------------------------------------------------------------------------------- 
    1201 \subsection[Equation of seawater (\forcode{nn_eos = {-1,1}})] 
    1202 {Equation of seawater (\protect\np{nn\_eos}\forcode{ = {-1,1}})} 
     1187\subsection[Equation of seawater (\texttt{ln}\{\texttt{\_teso10,\_eos80,\_seos}\})] 
     1188{Equation of seawater (\protect\np{ln\_teos10}, \protect\np{ln\_teos80}, or \protect\np{ln\_seos}) } 
    12031189\label{subsec:TRA_eos} 
     1190 
    12041191 
    12051192The Equation Of Seawater (EOS) is an empirical nonlinear thermodynamic relationship linking seawater density, 
     
    12181205\textit{(ii)}  it is more accurate, being based on an updated database of laboratory measurements, and 
    12191206\textit{(iii)} it uses Conservative Temperature and Absolute Salinity (instead of potential temperature and 
    1220 practical salinity for EOS-980, both variables being more suitable for use as model variables 
     1207practical salinity for EOS-80, both variables being more suitable for use as model variables 
    12211208\citep{ioc.iapso_bk10, graham.mcdougall_JPO13}. 
    12221209EOS-80 is an obsolescent feature of the \NEMO\ system, kept only for backward compatibility. 
     
    12301217density in the World Ocean varies by no more than 2$\%$ from that value \citep{gill_bk82}. 
    12311218 
    1232 Options are defined through the \nam{eos} namelist variables, and in particular \np{nn\_eos} which 
    1233 controls the EOS used (\forcode{= -1} for TEOS10 ; \forcode{= 0} for EOS-80 ; \forcode{= 1} for S-EOS). 
     1219Options which control the EOS used are defined through the \ngn{nameos} namelist variables. 
    12341220 
    12351221\begin{description} 
    1236 \item[\np{nn\_eos}\forcode{ = -1}] 
     1222\item[\np{ln\_teos10}\forcode{ = .true.}] 
    12371223  the polyTEOS10-bsq equation of seawater \citep{roquet.madec.ea_OM15} is used. 
    12381224  The accuracy of this approximation is comparable to the TEOS-10 rational function approximation, 
     
    12501236  In particular, the initial state deined by the user have to be given as \textit{Conservative} Temperature and 
    12511237  \textit{Absolute} Salinity. 
    1252   In addition, setting \np{ln\_useCT} to \forcode{.true.} convert the Conservative SST to potential SST prior to 
     1238  In addition, when using TEOS10, the Conservative SST is converted to potential SST prior to 
    12531239  either computing the air-sea and ice-sea fluxes (forced mode) or 
    12541240  sending the SST field to the atmosphere (coupled mode). 
    1255 \item[\np{nn\_eos}\forcode{ = 0}] 
     1241\item[\np{ln\_eos80}\forcode{ = .true.}] 
    12561242  the polyEOS80-bsq equation of seawater is used. 
    12571243  It takes the same polynomial form as the polyTEOS10, but the coefficients have been optimized to 
     
    12651251  Nevertheless, a severe assumption is made in order to have a heat content ($C_p T_p$) which 
    12661252  is conserved by the model: $C_p$ is set to a constant value, the TEOS10 value. 
    1267 \item[\np{nn\_eos}\forcode{ = 1}] 
     1253\item[\np{ln\_seos}\forcode{ = .true.}] 
    12681254  a simplified EOS (S-EOS) inspired by \citet{vallis_bk06} is chosen, 
    12691255  the coefficients of which has been optimized to fit the behavior of TEOS10 
     
    12751261  as well as between \textit{absolute} and \textit{practical} salinity. 
    12761262  S-EOS takes the following expression: 
     1263 
    12771264  \begin{gather*} 
    12781265    % \label{eq:tra_S-EOS} 
     
    13271314%        Brunt-V\"{a}is\"{a}l\"{a} Frequency 
    13281315% ------------------------------------------------------------------------------------------------------------- 
    1329 \subsection[Brunt-V\"{a}is\"{a}l\"{a} frequency (\forcode{nn_eos = [0-2]})] 
    1330 {Brunt-V\"{a}is\"{a}l\"{a} frequency (\protect\np{nn\_eos}\forcode{ = [0-2]})} 
     1316\subsection[Brunt-V\"{a}is\"{a}l\"{a} frequency] 
     1317{Brunt-V\"{a}is\"{a}l\"{a} frequency} 
    13311318\label{subsec:TRA_bn2} 
    13321319 
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