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Changeset 6275 for branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_TRA.tex – NEMO

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2016-02-01T03:35:04+01:00 (8 years ago)
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gm
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#1629: DOC of v3.6_stable. Upadate, see associated wiki page for description

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  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_TRA.tex

    r6039 r6275  
    3636(BBL) parametrisation, and an internal damping (DMP) term. The terms QSR,  
    3737BBC, BBL and DMP are optional. The external forcings and parameterisations  
    38 require complex inputs and complex calculations (e.g. bulk formulae, estimation  
     38require complex inputs and complex calculations ($e.g.$ bulk formulae, estimation  
    3939of mixing coefficients) that are carried out in the SBC, LDF and ZDF modules and  
    4040described in chapters \S\ref{SBC}, \S\ref{LDF} and  \S\ref{ZDF}, respectively.  
    41 Note that \mdl{tranpc}, the non-penetrative convection module,  although  
    42 (temporarily) located in the NEMO/OPA/TRA directory, is described with the  
    43 model vertical physics (ZDF). 
    44 %%% 
    45 \gmcomment{change the position of eosbn2 in the reference code} 
    46 %%% 
     41Note that \mdl{tranpc}, the non-penetrative convection module, although  
     42located in the NEMO/OPA/TRA directory as it directly modifies the tracer fields,  
     43is described with the model vertical physics (ZDF) together with other available  
     44parameterization of convection. 
    4745 
    4846In the present chapter we also describe the diagnostic equations used to compute  
    49 the sea-water properties (density, Brunt-Vais\"{a}l\"{a} frequency, specific heat and  
     47the sea-water properties (density, Brunt-V\"{a}is\"{a}l\"{a} frequency, specific heat and  
    5048freezing point with associated modules \mdl{eosbn2} and \mdl{phycst}). 
    5149 
     
    5654found in the \textit{trattt} or \textit{trattt\_xxx} module, in the NEMO/OPA/TRA directory. 
    5755 
    58 The user has the option of extracting each tendency term on the rhs of the tracer  
    59 equation for output (\key{trdtra} is defined), as described in Chap.~\ref{MISC}. 
     56The user has the option of extracting each tendency term on the RHS of the tracer  
     57equation for output (\np{ln\_tra\_trd} or \np{ln\_tra\_mxl}~=~true), as described in Chap.~\ref{DIA}. 
    6058 
    6159$\ $\newline    % force a new ligne 
     
    125123\end{description} 
    126124In all cases, this boundary condition retains local conservation of tracer.  
    127 Global conservation is obtained in both rigid-lid and non-linear free surface  
    128 cases, but not in the linear free surface case. Nevertheless, in the latter 
    129 case, it is achieved to a good approximation since the non-conservative  
     125Global conservation is obtained in non-linear free surface case,  
     126but \textit{not} in the linear free surface case. Nevertheless, in the latter case,  
     127it is achieved to a good approximation since the non-conservative  
    130128term is the product of the time derivative of the tracer and the free surface  
    131129height, two quantities that are not correlated (see \S\ref{PE_free_surface},  
     
    133131 
    134132The velocity field that appears in (\ref{Eq_tra_adv}) and (\ref{Eq_tra_adv_zco})  
    135 is the centred (\textit{now}) \textit{eulerian} ocean velocity (see Chap.~\ref{DYN}).  
    136 When eddy induced velocity (\textit{eiv}) parameterisation is used it is the \textit{now}  
    137 \textit{effective} velocity ($i.e.$ the sum of the eulerian and eiv velocities) which is used. 
     133is the centred (\textit{now}) \textit{effective} ocean velocity, $i.e.$ the \textit{eulerian} velocity 
     134(see Chap.~\ref{DYN}) plus the eddy induced velocity (\textit{eiv})  
     135and/or the mixed layer eddy induced velocity (\textit{eiv}) 
     136when those parameterisations are used (see Chap.~\ref{LDF}). 
    138137 
    139138The choice of an advection scheme is made in the \textit{\ngn{nam\_traadv}} namelist, by  
     
    146145 
    147146Note that  
    148 (1) cen2, cen4 and TVD schemes require an explicit diffusion  
     147(1) cen2 and TVD schemes require an explicit diffusion  
    149148operator while the other schemes are diffusive enough so that they do not  
    150149require additional diffusion ;  
    151 (2) cen2, cen4, MUSCL2, and UBS are not \textit{positive} schemes 
     150(2) cen2, MUSCL2, and UBS are not \textit{positive} schemes 
    152151\footnote{negative values can appear in an initially strictly positive tracer field  
    153152which is advected} 
     
    189188temperature is close to the freezing point). 
    190189This combined scheme has been included for specific grid points in the ORCA2  
    191 and ORCA4 configurations only. This is an obsolescent feature as the recommended  
     190configuration only. This is an obsolescent feature as the recommended  
    192191advection scheme for the ORCA configuration is TVD (see  \S\ref{TRA_adv_tvd}). 
    193192 
     
    196195have this order of accuracy. \gmcomment{Note also that ... blah, blah} 
    197196 
    198 % ------------------------------------------------------------------------------------------------------------- 
    199 %        4nd order centred scheme   
    200 % ------------------------------------------------------------------------------------------------------------- 
    201 \subsection   [$4^{nd}$ order centred scheme (cen4) (\np{ln\_traadv\_cen4})] 
    202            {$4^{nd}$ order centred scheme (cen4) (\np{ln\_traadv\_cen4}=true)} 
    203 \label{TRA_adv_cen4} 
    204  
    205 In the $4^{th}$ order formulation (to be implemented), tracer values are  
    206 evaluated at velocity points as a $4^{th}$ order interpolation, and thus depend on  
    207 the four neighbouring $T$-points. For example, in the $i$-direction: 
    208 \begin{equation} \label{Eq_tra_adv_cen4} 
    209 \tau _u^{cen4}  
    210 =\overline{   T - \frac{1}{6}\,\delta _i \left[ \delta_{i+1/2}[T] \,\right]   }^{\,i+1/2} 
    211 \end{equation} 
    212  
    213 Strictly speaking, the cen4 scheme is not a $4^{th}$ order advection scheme  
    214 but a $4^{th}$ order evaluation of advective fluxes, since the divergence of  
    215 advective fluxes \eqref{Eq_tra_adv} is kept at $2^{nd}$ order. The phrase ``$4^{th}$  
    216 order scheme'' used in oceanographic literature is usually associated  
    217 with the scheme presented here. Introducing a \textit{true} $4^{th}$ order advection  
    218 scheme is feasible but, for consistency reasons, it requires changes in the  
    219 discretisation of the tracer advection together with changes in both the  
    220 continuity equation and the momentum advection terms.   
    221  
    222 A direct consequence of the pseudo-fourth order nature of the scheme is that  
    223 it is not non-diffusive, i.e. the global variance of a tracer is not preserved using  
    224 \textit{cen4}. Furthermore, it must be used in conjunction with an explicit  
    225 diffusion operator to produce a sensible solution. The time-stepping is also  
    226 performed using a leapfrog scheme in conjunction with an Asselin time-filter,  
    227 so $T$ in (\ref{Eq_tra_adv_cen4}) is the \textit{now} tracer. 
    228  
    229 At a $T$-grid cell adjacent to a boundary (coastline, bottom and surface), an  
    230 additional hypothesis must be made to evaluate $\tau _u^{cen4}$. This  
    231 hypothesis usually reduces the order of the scheme. Here we choose to set  
    232 the gradient of $T$ across the boundary to zero. Alternative conditions can be  
    233 specified, such as a reduction to a second order scheme for these near boundary  
    234 grid points. 
    235197 
    236198% ------------------------------------------------------------------------------------------------------------- 
     
    270232used for the diffusive part.  
    271233 
     234An additional option has been added controlled by \np{ln\_traadv\_tvd\_zts}.  
     235By setting this logical to true, a TVD scheme is used on both horizontal and vertical direction,  
     236but on the latter, a split-explicit time stepping is used, with 5 sub-timesteps.  
     237This option can be useful when the value of the timestep is limited by vertical advection \citep{Lemarie_OM2015}.  
     238Note that in this case, a similar split-explicit time stepping should be used on  
     239vertical advection of momentum to ensure a better stability (see \np{ln\_dynzad\_zts} in \S\ref{DYN_zad}). 
     240 
     241 
    272242% ------------------------------------------------------------------------------------------------------------- 
    273243%        MUSCL scheme   
     
    296266 
    297267For an ocean grid point adjacent to land and where the ocean velocity is  
    298 directed toward land, two choices are available: an upstream flux  
    299 (\np{ln\_traadv\_muscl}=true) or a second order flux  
    300 (\np{ln\_traadv\_muscl2}=true). Note that the latter choice does not ensure  
    301 the \textit{positive} character of the scheme. Only the former can be used  
    302 on both active and passive tracers. The two MUSCL schemes are implemented  
    303 in the \mdl{traadv\_tvd} and \mdl{traadv\_tvd2} modules. 
     268directed toward land, two choices are available: an upstream flux (\np{ln\_traadv\_muscl}=true)  
     269or a second order flux (\np{ln\_traadv\_muscl2}=true).  
     270Note that the latter choice does not ensure the \textit{positive} character of the scheme.  
     271Only the former can be used on both active and passive tracers.  
     272The two MUSCL schemes are implemented in the \mdl{traadv\_tvd} and \mdl{traadv\_tvd2} modules. 
     273 
     274Note that when using np{ln\_traadv\_msc\_ups}~=~true in addition to \np{ln\_traadv\_muscl}=true,  
     275the MUSCL fluxes are replaced by upstream fluxes in vicinity of river mouths. 
    304276 
    305277% ------------------------------------------------------------------------------------------------------------- 
     
    416388direction (as for the UBS case) should be implemented to restore this property. 
    417389 
    418  
    419 % ------------------------------------------------------------------------------------------------------------- 
    420 %        PPM scheme   
    421 % ------------------------------------------------------------------------------------------------------------- 
    422 \subsection   [Piecewise Parabolic Method (PPM) (\np{ln\_traadv\_ppm})] 
    423          {Piecewise Parabolic Method (PPM) (\np{ln\_traadv\_ppm}=true)} 
    424 \label{TRA_adv_ppm} 
    425  
    426 The Piecewise Parabolic Method (PPM) proposed by Colella and Woodward (1984)  
    427 \sgacomment{reference?} 
    428 is based on a quadradic piecewise construction. Like the QCK scheme, it is associated  
    429 with the ULTIMATE QUICKEST limiter \citep{Leonard1991}. It has been implemented  
    430 in \NEMO by G. Reffray (MERCATOR-ocean) but is not yet offered in the reference  
    431 version 3.3. 
    432390 
    433391% ================================================================ 
     
    464422surfaces is given by:  
    465423\begin{equation} \label{Eq_tra_ldf_lap} 
    466 D_T^{lT} =\frac{1}{b_tT} \left( \; 
     424D_T^{lT} =\frac{1}{b_t} \left( \; 
    467425   \delta _{i}\left[ A_u^{lT} \; \frac{e_{2u}\,e_{3u}}{e_{1u}} \;\delta _{i+1/2} [T] \right]  
    468426+ \delta _{j}\left[ A_v^{lT} \;  \frac{e_{1v}\,e_{3v}}{e_{2v}} \;\delta _{j+1/2} [T] \right]  \;\right) 
     
    661619the thickness of the top model layer.  
    662620 
    663 Due to interactions and mass exchange of water ($F_{mass}$) with other Earth system components ($i.e.$ atmosphere, sea-ice, land), 
    664 the change in the heat and salt content of the surface layer of the ocean is due both  
    665 to the heat and salt fluxes crossing the sea surface (not linked with $F_{mass}$) 
    666  and to the heat and salt content of the mass exchange. 
    667 \sgacomment{ the following does not apply to the release to which this documentation is  
    668 attached and so should not be included .... 
    669 In a forthcoming release, these two parts, computed in the surface module (SBC), will be included directly 
    670 in $Q_{ns}$, the surface heat flux and $F_{salt}$, the surface salt flux. 
    671 The specification of these fluxes is further detailed in the SBC chapter (see \S\ref{SBC}).  
    672 This change will provide a forcing formulation which is the same for any tracer (including temperature and salinity). 
    673   
    674 In the current version, the situation is a little bit more complicated. } 
     621Due to interactions and mass exchange of water ($F_{mass}$) with other Earth system components  
     622($i.e.$ atmosphere, sea-ice, land), the change in the heat and salt content of the surface layer  
     623of the ocean is due both to the heat and salt fluxes crossing the sea surface (not linked with $F_{mass}$)  
     624and to the heat and salt content of the mass exchange. They are both included directly in $Q_{ns}$,  
     625the surface heat flux, and $F_{salt}$, the surface salt flux (see \S\ref{SBC} for further details). 
     626By doing this, the forcing formulation is the same for any tracer (including temperature and salinity). 
    675627 
    676628The surface module (\mdl{sbcmod}, see \S\ref{SBC}) provides the following  
     
    679631$\bullet$ $Q_{ns}$, the non-solar part of the net surface heat flux that crosses the sea surface  
    680632(i.e. the difference between the total surface heat flux and the fraction of the short wave flux that  
    681 penetrates into the water column, see \S\ref{TRA_qsr}) 
    682  
    683 $\bullet$ \textit{emp}, the mass flux exchanged with the atmosphere (evaporation minus precipitation) 
    684  
    685 $\bullet$ $\textit{emp}_S$, an equivalent mass flux taking into account the effect of ice-ocean mass exchange 
    686  
    687 $\bullet$ \textit{rnf}, the mass flux associated with runoff (see \S\ref{SBC_rnf} for further detail of how it acts on temperature and salinity tendencies) 
    688  
    689 The $\textit{emp}_S$ field is not simply the budget of evaporation-precipitation+freezing-melting because  
    690 the sea-ice is not currently embedded in the ocean but levitates above it. There is no mass 
    691 exchanged between the sea-ice and the ocean. Instead we only take into account the salt 
    692 flux associated with the non-zero salinity of sea-ice, and the concentration/dilution effect 
    693 due to the freezing/melting (F/M) process. These two parts of the forcing are then converted into  
    694 an equivalent mass flux given by $\textit{emp}_S - \textit{emp}$. As a result of this mess,  
    695 the surface boundary condition on temperature and salinity is applied as follows: 
    696  
    697 In the nonlinear free surface case (\key{vvl} is defined): 
     633penetrates into the water column, see \S\ref{TRA_qsr}) plus the heat content associated with  
     634of the mass exchange with the atmosphere and lands. 
     635 
     636$\bullet$ $\textit{sfx}$, the salt flux resulting from ice-ocean mass exchange (freezing, melting, ridging...) 
     637 
     638$\bullet$ \textit{emp}, the mass flux exchanged with the atmosphere (evaporation minus precipitation)  
     639 and possibly with the sea-ice and ice-shelves. 
     640 
     641$\bullet$ \textit{rnf}, the mass flux associated with runoff  
     642(see \S\ref{SBC_rnf} for further detail of how it acts on temperature and salinity tendencies) 
     643 
     644In the non-linear free surface case (\key{vvl} is defined), the surface boundary condition  
     645on temperature and salinity is applied as follows: 
    698646\begin{equation} \label{Eq_tra_sbc} 
     647\begin{aligned} 
     648 &F^T = \frac{ 1 }{\rho _o \;C_p \,\left. e_{3t} \right|_{k=1} }  &\overline{ Q_{ns}       }^t  & \\  
     649& F^S =\frac{ 1 }{\rho _o  \,      \left. e_{3t} \right|_{k=1} }  &\overline{ \textit{sfx} }^t   & \\    
     650 \end{aligned} 
     651\end{equation}  
     652where $\overline{x }^t$ means that $x$ is averaged over two consecutive time steps  
     653($t-\rdt/2$ and $t+\rdt/2$). Such time averaging prevents the  
     654divergence of odd and even time step (see \S\ref{STP}). 
     655 
     656In the linear free surface case (\key{vvl} is \textit{not} defined),  
     657an additional term has to be added on both temperature and salinity.  
     658On temperature, this term remove the heat content associated with mass exchange 
     659that has been added to $Q_{ns}$. On salinity, this term mimics the concentration/dilution effect that 
     660would have resulted from a change in the volume of the first level. 
     661The resulting surface boundary condition is applied as follows: 
     662\begin{equation} \label{Eq_tra_sbc_lin} 
    699663\begin{aligned} 
    700664 &F^T = \frac{ 1 }{\rho _o \;C_p \,\left. e_{3t} \right|_{k=1} }    
     
    702666% 
    703667& F^S =\frac{ 1 }{\rho _o \,\left. e_{3t} \right|_{k=1} }  
    704            &\overline{ \left( (\textit{emp}_S - \textit{emp})\;\left. S \right|_{k=1}  \right) }^t   & \\    
     668           &\overline{ \left( \;\textit{sfx} - \textit{emp} \;\left. S \right|_{k=1}  \right) }^t   & \\    
    705669 \end{aligned} 
    706670\end{equation}  
    707  
    708 In the linear free surface case (\key{vvl} not defined): 
    709 \begin{equation} \label{Eq_tra_sbc_lin} 
    710 \begin{aligned} 
    711  &F^T = \frac{ 1 }{\rho _o \;C_p \,\left. e_{3t} \right|_{k=1} }  &\overline{ Q_{ns} }^t  & \\  
    712 % 
    713 & F^S =\frac{ 1 }{\rho _o \,\left. e_{3t} \right|_{k=1} }  
    714            &\overline{ \left( \textit{emp}_S\;\left. S \right|_{k=1}  \right) }^t   & \\    
    715  \end{aligned} 
    716 \end{equation}  
    717 where $\overline{x }^t$ means that $x$ is averaged over two consecutive time steps  
    718 ($t-\rdt/2$ and $t+\rdt/2$). Such time averaging prevents the  
    719 divergence of odd and even time step (see \S\ref{STP}). 
    720  
    721 The two set of equations, \eqref{Eq_tra_sbc} and \eqref{Eq_tra_sbc_lin}, are obtained  
    722 by assuming that the temperature of precipitation and evaporation are equal to 
    723 the ocean surface temperature and that their salinity is zero. Therefore, the heat content 
    724 of the \textit{emp} budget must be added to the temperature equation in the variable volume case,  
    725 while it does not appear in the constant volume case. Similarly, the \textit{emp} budget affects  
    726 the ocean surface salinity in the constant volume case (through the concentration dilution effect) 
    727 while it does not appears explicitly in the variable volume case since salinity change will be 
    728 induced by volume change. In both constant and variable volume cases, surface salinity  
    729 will change with ice-ocean salt flux and F/M flux (both contained in $\textit{emp}_S - \textit{emp}$) without mass exchanges. 
    730  
    731 Note that the concentration/dilution effect due to F/M is computed using 
    732 a constant ice salinity as well as a constant ocean salinity.  
    733 This approximation suppresses the correlation between \textit{SSS}  
    734 and F/M flux, allowing the ice-ocean salt exchanges to be conservative. 
    735 Indeed, if this approximation is not made, even if the F/M budget is zero  
    736 on average over the whole ocean domain and over the seasonal cycle,  
    737 the associated salt flux is not zero, since sea-surface salinity and F/M flux are  
    738 intrinsically correlated (high \textit{SSS} are found where freezing is  
    739 strong whilst low \textit{SSS} is usually associated with high melting areas). 
    740  
    741 Even using this approximation, an exact conservation of heat and salt content  
    742 is only achieved in the variable volume case. In the constant volume case,  
    743 there is a small imbalance associated with the product $(\partial_t\eta - \textit{emp}) * \textit{SSS}$. 
    744 Nevertheless, the salt content variation is quite small and will not induce 
    745 a long term drift as there is no physical reason for $(\partial_t\eta - \textit{emp})$  
    746 and \textit{SSS} to be correlated \citep{Roullet_Madec_JGR00}.  
    747 Note that, while quite small, the imbalance in the constant volume case is larger  
     671Note that an exact conservation of heat and salt content is only achieved with non-linear free surface.  
     672In the linear free surface case, there is a small imbalance. The imbalance is larger  
    748673than the imbalance associated with the Asselin time filter \citep{Leclair_Madec_OM09}.  
    749 This is the reason why the modified filter is not applied in the constant volume case. 
     674This is the reason why the modified filter is not applied in the linear free surface case (see \S\ref{STP}). 
    750675 
    751676% ------------------------------------------------------------------------------------------------------------- 
     
    11031028\subsection[DMP\_TOOLS]{Generating resto.nc using DMP\_TOOLS} 
    11041029 
    1105 DMP\_TOOLS can be used to generate a netcdf file containing the restoration coefficient $\gamma$. Note that in order to maintain bit comparison with previous NEMO versions DMP\_TOOLS must be compiled and run on the same machine as the NEMO model. A mesh\_mask.nc file for the model configuration is required as an input. This can be generated by carrying out a short model run with the namelist parameter \np{nn\_msh} set to 1. The namelist parameter \np{ln\_tradmp} will also need to be set to .false. for this to work. The \nl{nam\_dmp\_create} namelist in the DMP\_TOOLS directory is used to specify options for the restoration coefficient. 
     1030DMP\_TOOLS can be used to generate a netcdf file containing the restoration coefficient $\gamma$.  
     1031Note that in order to maintain bit comparison with previous NEMO versions DMP\_TOOLS must be compiled  
     1032and run on the same machine as the NEMO model. A mesh\_mask.nc file for the model configuration is required as an input.  
     1033This can be generated by carrying out a short model run with the namelist parameter \np{nn\_msh} set to 1.  
     1034The namelist parameter \np{ln\_tradmp} will also need to be set to .false. for this to work.  
     1035The \nl{nam\_dmp\_create} namelist in the DMP\_TOOLS directory is used to specify options for the restoration coefficient. 
    11061036 
    11071037%--------------------------------------------nam_dmp_create------------------------------------------------- 
     
    11111041\np{cp\_cfg}, \np{cp\_cpz}, \np{jp\_cfg} and \np{jperio} specify the model configuration being used and should be the same as specified in \nl{namcfg}. The variable \nl{lzoom} is used to specify that the damping is being used as in case \textit{a} above to provide boundary conditions to a zoom configuration. In the case of the arctic or antarctic zoom configurations this includes some specific treatment. Otherwise damping is applied to the 6 grid points along the ocean boundaries. The open boundaries are specified by the variables \np{lzoom\_n}, \np{lzoom\_e}, \np{lzoom\_s}, \np{lzoom\_w} in the \nl{nam\_zoom\_dmp} name list. 
    11121042 
    1113 The remaining switch namelist variables determine the spatial variation of the restoration coefficient in non-zoom configurations. \np{ln\_full\_field} specifies that newtonian damping should be applied to the whole model domain. \np{ln\_med\_red\_seas} specifies grid specific restoration coefficients in the Mediterranean Sea for the ORCA4, ORCA2 and ORCA05 configurations. If \np{ln\_old\_31\_lev\_code} is set then the depth variation of the coeffients will be specified as a function of the model number. This option is included to allow backwards compatability of the ORCA2 reference configurations with previous model versions. \np{ln\_coast} specifies that the restoration coefficient should be reduced near to coastlines. This option only has an effect if \np{ln\_full\_field} is true. \np{ln\_zero\_top\_layer} specifies that the restoration coefficient should be zero in the surface layer. Finally \np{ln\_custom} specifies that the custom module will be called. This module is contained in the file custom.F90 and can be edited by users. For example damping could be applied in a specific region. 
    1114  
    1115 The restoration coefficient can be set to zero in equatorial regions by specifying a positive value of \np{nn\_hdmp}. Equatorward of this latitude the restoration coefficient will be zero with a smooth transition to the full values of a 10$^{\circ}$ latitud band. This is often used because of the short adjustment time scale in the equatorial region \citep{Reverdin1991, Fujio1991, Marti_PhD92}. The time scale associated with the damping depends on the depth as a hyperbolic tangent, with \np{rn\_surf} as surface value, \np{rn\_bot} as bottom value and a transition depth of \np{rn\_dep}.   
     1043The remaining switch namelist variables determine the spatial variation of the restoration coefficient in non-zoom configurations.  
     1044\np{ln\_full\_field} specifies that newtonian damping should be applied to the whole model domain.  
     1045\np{ln\_med\_red\_seas} specifies grid specific restoration coefficients in the Mediterranean Sea  
     1046for the ORCA4, ORCA2 and ORCA05 configurations.  
     1047If \np{ln\_old\_31\_lev\_code} is set then the depth variation of the coeffients will be specified as  
     1048a function of the model number. This option is included to allow backwards compatability of the ORCA2 reference  
     1049configurations with previous model versions.  
     1050\np{ln\_coast} specifies that the restoration coefficient should be reduced near to coastlines.  
     1051This option only has an effect if \np{ln\_full\_field} is true.  
     1052\np{ln\_zero\_top\_layer} specifies that the restoration coefficient should be zero in the surface layer.  
     1053Finally \np{ln\_custom} specifies that the custom module will be called.  
     1054This module is contained in the file custom.F90 and can be edited by users. For example damping could be applied in a specific region. 
     1055 
     1056The restoration coefficient can be set to zero in equatorial regions by specifying a positive value of \np{nn\_hdmp}.  
     1057Equatorward of this latitude the restoration coefficient will be zero with a smooth transition to  
     1058the full values of a 10$^{\circ}$ latitud band.  
     1059This is often used because of the short adjustment time scale in the equatorial region  
     1060\citep{Reverdin1991, Fujio1991, Marti_PhD92}. The time scale associated with the damping depends on the depth as a  
     1061hyperbolic tangent, with \np{rn\_surf} as surface value, \np{rn\_bot} as bottom value and a transition depth of \np{rn\_dep}.   
    11161062 
    11171063% ================================================================ 
     
    12651211\hline 
    12661212coeff.   & computer name   & S-EOS     &  description                      \\ \hline 
    1267 $a_0$       & \np{nn\_a0}     & 1.6550 $10^{-1}$ &  linear thermal expansion coeff.    \\ \hline 
    1268 $b_0$       & \np{nn\_b0}     & 7.6554 $10^{-1}$ &  linear haline  expansion coeff.    \\ \hline 
    1269 $\lambda_1$ & \np{nn\_lambda1}& 5.9520 $10^{-2}$ &  cabbeling coeff. in $T^2$          \\ \hline 
    1270 $\lambda_2$ & \np{nn\_lambda2}& 5.4914 $10^{-4}$ &  cabbeling coeff. in $S^2$       \\ \hline 
    1271 $\nu$       & \np{nn\_nu}     & 2.4341 $10^{-3}$ &  cabbeling coeff. in $T \, S$       \\ \hline 
    1272 $\mu_1$     & \np{nn\_mu1}    & 1.4970 $10^{-4}$ &  thermobaric coeff. in T         \\ \hline 
    1273 $\mu_2$     & \np{nn\_mu2}    & 1.1090 $10^{-5}$ &  thermobaric coeff. in S            \\ \hline 
     1213$a_0$       & \np{rn\_a0}     & 1.6550 $10^{-1}$ &  linear thermal expansion coeff.    \\ \hline 
     1214$b_0$       & \np{rn\_b0}     & 7.6554 $10^{-1}$ &  linear haline  expansion coeff.    \\ \hline 
     1215$\lambda_1$ & \np{rn\_lambda1}& 5.9520 $10^{-2}$ &  cabbeling coeff. in $T^2$          \\ \hline 
     1216$\lambda_2$ & \np{rn\_lambda2}& 5.4914 $10^{-4}$ &  cabbeling coeff. in $S^2$       \\ \hline 
     1217$\nu$       & \np{rn\_nu}     & 2.4341 $10^{-3}$ &  cabbeling coeff. in $T \, S$       \\ \hline 
     1218$\mu_1$     & \np{rn\_mu1}    & 1.4970 $10^{-4}$ &  thermobaric coeff. in T         \\ \hline 
     1219$\mu_2$     & \np{rn\_mu2}    & 1.1090 $10^{-5}$ &  thermobaric coeff. in S            \\ \hline 
    12741220\end{tabular} 
    12751221\caption{ \label{Tab_SEOS} 
     
    12811227 
    12821228% ------------------------------------------------------------------------------------------------------------- 
    1283 %        Brunt-Vais\"{a}l\"{a} Frequency 
    1284 % ------------------------------------------------------------------------------------------------------------- 
    1285 \subsection{Brunt-Vais\"{a}l\"{a} Frequency (\np{nn\_eos} = 0, 1 or 2)} 
     1229%        Brunt-V\"{a}is\"{a}l\"{a} Frequency 
     1230% ------------------------------------------------------------------------------------------------------------- 
     1231\subsection{Brunt-V\"{a}is\"{a}l\"{a} Frequency (\np{nn\_eos} = 0, 1 or 2)} 
    12861232\label{TRA_bn2} 
    12871233 
    1288 An accurate computation of the ocean stability (i.e. of $N$, the brunt-Vais\"{a}l\"{a} 
     1234An accurate computation of the ocean stability (i.e. of $N$, the brunt-V\"{a}is\"{a}l\"{a} 
    12891235 frequency) is of paramount importance as determine the ocean stratification and  
    12901236 is used in several ocean parameterisations (namely TKE, GLS, Richardson number dependent  
     
    13021248function that can be found in \mdl{eosbn2}. 
    13031249 
    1304  
    1305 % ------------------------------------------------------------------------------------------------------------- 
    1306 %        Potential Energy      
    1307 % ------------------------------------------------------------------------------------------------------------- 
    1308 %\subsection{Potential Energy anomalies} 
    1309 %\label{TRA_bn2} 
    1310  
    1311 %    =====>>>>> TO BE written 
    1312 % 
    1313  
    13141250% ------------------------------------------------------------------------------------------------------------- 
    13151251%        Freezing Point of Seawater 
     
    13411277\label{TRA_zpshde} 
    13421278 
    1343 \gmcomment{STEVEN: to be consistent with earlier discussion of differencing and averaging operators, I've changed "derivative" to "difference" and "mean" to "average"} 
     1279\gmcomment{STEVEN: to be consistent with earlier discussion of differencing and averaging operators,  
     1280                   I've changed "derivative" to "difference" and "mean" to "average"} 
    13441281 
    13451282With partial bottom cells (\np{ln\_zps}=true), in general, tracers in horizontally  
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