Changeset 11459
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 20190820T10:59:40+02:00 (13 months ago)
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NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex
r11435 r11459 48 48 associated modules \mdl{eosbn2} and \mdl{phycst}). 49 49 50 The different options available to the user are managed by namelist logicals or CPP keys.50 The different options available to the user are managed by namelist logicals. 51 51 For each equation term \textit{TTT}, the namelist logicals are \textit{ln\_traTTT\_xxx}, 52 52 where \textit{xxx} is a 3 or 4 letter acronym corresponding to each optional scheme. 53 %The CPP key (when it exists) is \key{traTTT}.54 53 The equivalent code can be found in the \textit{traTTT} or \textit{traTTT\_xxx} module, 55 54 in the \path{./src/OCE/TRA} directory. … … 69 68 % 70 69 71 When considered (\ie\ when \np{ln\_traadv\_ NONE} is not set to \forcode{.true.}),70 When considered (\ie\ when \np{ln\_traadv\_OFF} is not set to \forcode{.true.}), 72 71 the advection tendency of a tracer is expressed in flux form, 73 72 \ie\ as the divergence of the advective fluxes. … … 140 139 two quantities that are not correlated \citep{roullet.madec_JGR00, griffies.pacanowski.ea_MWR01, campin.adcroft.ea_OM04}. 141 140 142 The velocity field that appears in (\autoref{eq:tra_adv} and \autoref{eq:tra_adv_zco?}) is141 The velocity field that appears in (\autoref{eq:tra_adv} is 143 142 the centred (\textit{now}) \textit{effective} ocean velocity, \ie\ the \textit{eulerian} velocity 144 143 (see \autoref{chap:DYN}) plus the eddy induced velocity (\textit{eiv}) and/or … … 287 286 A comparison of FCT2 with MUSCL and a MPDATA scheme can be found in \citet{levy.estublier.ea_GRL01}. 288 287 289 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 splitexplicit time stepping is used, with a number of subtimestep 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 splitexplicit time stepping should be used on vertical advection of momentum to295 insure a better stability (see \autoref{subsec:DYN_zad}).296 288 297 289 For stability reasons (see \autoref{chap:STP}), … … 375 367 \citep{shchepetkin.mcwilliams_OM05, demange_phd14}. 376 368 Therefore 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}). 378 370 379 371 For stability reasons (see \autoref{chap:STP}), the first term in \autoref{eq:tra_adv_ubs} … … 467 459 % Type of operator 468 460 %  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}) } 471 463 \label{subsec:TRA_ldf_op} 472 464 … … 474 466 475 467 \begin{description} 476 \item[\np{ln\_traldf\_ NONE}\forcode{ = .true.}:]468 \item[\np{ln\_traldf\_OFF}\forcode{ = .true.}:] 477 469 no operator selected, the lateral diffusive tendency will not be applied to the tracer equation. 478 470 This option can be used when the selected advection scheme is diffusive enough (MUSCL scheme for example). … … 542 534 where zero diffusive fluxes is assumed across solid boundaries, 543 535 first (and third in bilaplacian case) horizontal tracer derivative are masked. 544 It is implemented in the \rou{tra ldf\_lap} subroutine found in the \mdl{traldf\_lap} module.545 The module also contains \rou{tra ldf\_blp}, the subroutine calling twice \rou{traldf\_lap} in order to536 It is implemented in the \rou{tra\_ldf\_lap} subroutine found in the \mdl{traldf\_lap\_blp}} module. 537 The module also contains \rou{tra\_ldf\_blp}, the subroutine calling twice \rou{tra\_ldf\_lap} in order to 546 538 compute the isolevel bilaplacian operator. 547 539 548 It is a \textit{horizontal} operator (\ie \acting along geopotential surfaces) in540 It is a \textit{horizontal} operator (\ie acting along geopotential surfaces) in 549 541 the $z$coordinate with or without partial steps, but is simply an isolevel operator in the $s$coordinate. 550 542 It is thus used when, in addition to \np{ln\_traldf\_lap} or \np{ln\_traldf\_blp}\forcode{ = .true.}, … … 614 606 \label{subsec:TRA_ldf_triad} 615 607 616 If the Griffies triad scheme is employed (\np{ln\_traldf\_triad}\forcode{ = .true.}; see \autoref{apdx:triad})617 618 608 An 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.}).609 is also available in \NEMO\ (\np{ln\_traldf\_triad}\forcode{ = .true.}). 620 610 A complete description of the algorithm is given in \autoref{apdx:triad}. 621 611 … … 665 655 respectively. 666 656 Generally, $A_w^{vT} = A_w^{vS}$ except when double diffusive mixing is parameterised 667 (\ie\ \ texttt{zdfddm?} is defined).657 (\ie\ \np{ln\_zdfddm} equals \forcode{.true.},). 668 658 The way these coefficients are evaluated is given in \autoref{chap:ZDF} (ZDF). 669 659 Furthermore, when isoneutral mixing is used, both mixing coefficients are increased by … … 677 667 678 668 The 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 669 there would be too restrictive constraint on the time step if we use explicit time stepping. 670 Therefore an implicit time stepping is preferred for the vertical diffusion since 682 671 it overcomes the stability constraint. 683 A forward time differencing scheme (\np{ln\_zdfexp}\forcode{ = .true.}) using684 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.686 672 687 673 % ================================================================ … … 777 763 778 764 Options are defined through the \nam{tra\_qsr} namelist variables. 779 When the penetrative solar radiation option is used (\np{ln\_ flxqsr}\forcode{ = .true.}),765 When the penetrative solar radiation option is used (\np{ln\_traqsr}\forcode{ = .true.}), 780 766 the 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.767 If it is not used (\np{ln\_traqsr}\forcode{ = .false.}) all the heat flux is absorbed in the first ocean level. 782 768 Thus, in the former case a term is added to the time evolution equation of temperature \autoref{eq:PE_tra_T} and 783 769 the surface boundary condition is modified to take into account only the nonpenetrative part of the surface … … 843 829 844 830 \begin{description} 845 \item[\np{nn\_ch dta}\forcode{ = 0}]831 \item[\np{nn\_chldta}\forcode{ = 0}] 846 832 a constant 0.05 g.Chl/L value everywhere ; 847 \item[\np{nn\_ch dta}\forcode{ = 1}]833 \item[\np{nn\_chldta}\forcode{ = 1}] 848 834 an observed time varying chlorophyll deduced from satellite surface ocean color measurement spread uniformly in 849 835 the vertical direction; 850 \item[\np{nn\_ch dta}\forcode{ = 2}]836 \item[\np{nn\_chldta}\forcode{ = 2}] 851 837 same as previous case except that a vertical profile of chlorophyl is used. 852 838 Following \cite{morel.berthon_LO89}, the profile is computed from the local surface chlorophyll value; … … 854 840 simulated time varying chlorophyll by TOP biogeochemical model. 855 841 In this case, the RGB formulation is used to calculate both the phytoplankton light limitation in 856 PISCES or LOBSTERand the oceanic heating rate.842 PISCES and the oceanic heating rate. 857 843 \end{description} 858 844 … … 890 876 % Bottom Boundary Condition 891 877 %  892 \subsection[Bottom boundary condition (\textit{trabbc.F90}) ]878 \subsection[Bottom boundary condition (\textit{trabbc.F90})  \forcode{ln_trabbc = .true.})] 893 879 {Bottom boundary condition (\protect\mdl{trabbc})} 894 880 \label{subsec:TRA_bbc} … … 919 905 (\ie\ the one associated with the Antarctic Bottom Water) by a few Sverdrups \citep{emilegeay.madec_OS09}. 920 906 921 Options are defined through the \nam{ tra\_bbc} namelist variables.907 Options are defined through the \nam{bbc} namelist variables. 922 908 The presence of geothermal heating is controlled by setting the namelist parameter \np{ln\_trabbc} to true. 923 909 Then, 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.910 the \np{rn\_geoflx\_cst}, which is also a namelist parameter. 925 911 When \np{nn\_geoflx} is set to 2, a spatially varying geothermal heat flux is introduced which is provided in 926 912 the \ifile{geothermal\_heating} NetCDF file (\autoref{fig:geothermal}) \citep{emilegeay.madec_OS09}. … … 1114 1100 Options are defined through the \nam{tra\_dmp} namelist variables. 1115 1101 The 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 in1102 It also requires that both \np{ln\_tsd\_init} and \np{ln\_tsd\_dmp} are set to true in 1117 1103 \nam{tsd} namelist as well as \np{sn\_tem} and \np{sn\_sal} structures are correctly set 1118 1104 (\ie\ that $T_o$ and $S_o$ are provided in input files and read using \mdl{fldread}, … … 1175 1161 Its default value is \np{rn\_atfp}\forcode{ = 10.e3}. 1176 1162 Note that the forcing correction term in the filter is not applied in linear free surface 1177 (\jp{l k\_vvl}\forcode{ = .false.}) (see \autoref{subsec:TRA_sbc}).1163 (\jp{ln\_linssh}\forcode{ = .true.}) (see \autoref{subsec:TRA_sbc}). 1178 1164 Not also that in constant volume case, the time stepping is performed on $T$, not on its content, $e_{3t}T$. 1179 1165 … … 1199 1185 % Equation of State 1200 1186 %  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}) } 1203 1189 \label{subsec:TRA_eos} 1190 1204 1191 1205 1192 The Equation Of Seawater (EOS) is an empirical nonlinear thermodynamic relationship linking seawater density, … … 1218 1205 \textit{(ii)} it is more accurate, being based on an updated database of laboratory measurements, and 1219 1206 \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 variables1207 practical salinity for EOS80, both variables being more suitable for use as model variables 1221 1208 \citep{ioc.iapso_bk10, graham.mcdougall_JPO13}. 1222 1209 EOS80 is an obsolescent feature of the \NEMO\ system, kept only for backward compatibility. … … 1230 1217 density in the World Ocean varies by no more than 2$\%$ from that value \citep{gill_bk82}. 1231 1218 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 EOS80 ; \forcode{= 1} for SEOS). 1219 Options which control the EOS used are defined through the \ngn{nameos} namelist variables. 1234 1220 1235 1221 \begin{description} 1236 \item[\np{ nn\_eos}\forcode{ = 1}]1222 \item[\np{ln\_teos10}\forcode{ = .true.}] 1237 1223 the polyTEOS10bsq equation of seawater \citep{roquet.madec.ea_OM15} is used. 1238 1224 The accuracy of this approximation is comparable to the TEOS10 rational function approximation, … … 1250 1236 In particular, the initial state deined by the user have to be given as \textit{Conservative} Temperature and 1251 1237 \textit{Absolute} Salinity. 1252 In addition, setting \np{ln\_useCT} to \forcode{.true.} convert the Conservative SSTto potential SST prior to1238 In addition, when using TEOS10, the Conservative SST is converted to potential SST prior to 1253 1239 either computing the airsea and icesea fluxes (forced mode) or 1254 1240 sending the SST field to the atmosphere (coupled mode). 1255 \item[\np{ nn\_eos}\forcode{ = 0}]1241 \item[\np{ln\_eos80}\forcode{ = .true.}] 1256 1242 the polyEOS80bsq equation of seawater is used. 1257 1243 It takes the same polynomial form as the polyTEOS10, but the coefficients have been optimized to … … 1265 1251 Nevertheless, a severe assumption is made in order to have a heat content ($C_p T_p$) which 1266 1252 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.}] 1268 1254 a simplified EOS (SEOS) inspired by \citet{vallis_bk06} is chosen, 1269 1255 the coefficients of which has been optimized to fit the behavior of TEOS10 … … 1275 1261 as well as between \textit{absolute} and \textit{practical} salinity. 1276 1262 SEOS takes the following expression: 1263 1277 1264 \begin{gather*} 1278 1265 % \label{eq:tra_SEOS} … … 1327 1314 % BruntV\"{a}is\"{a}l\"{a} Frequency 1328 1315 %  1329 \subsection[BruntV\"{a}is\"{a}l\"{a} frequency (\forcode{nn_eos = [02]})]1330 {BruntV\"{a}is\"{a}l\"{a} frequency (\protect\np{nn\_eos}\forcode{ = [02]})}1316 \subsection[BruntV\"{a}is\"{a}l\"{a} frequency] 1317 {BruntV\"{a}is\"{a}l\"{a} frequency} 1331 1318 \label{subsec:TRA_bn2} 1332 1319
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