2014-08-14T17:18:46+02:00 (7 years ago)

Modified documentation to describe new features.

1 edited


  • branches/2014/dev_r4650_UKMO3_masked_damping/DOC/TexFiles/Chapters/Chap_TRA.tex

    r4147 r4745  
    10771077correctly set  ($i.e.$ that $T_o$ and $S_o$ are provided in input files and read  
    10781078using \mdl{fldread}, see \S\ref{SBC_fldread}).  
    1079 The restoring coefficient $\gamma$ is a three-dimensional array initialized by the  
    1080 user in routine \rou{dtacof} also located in module \mdl{tradmp}.  
     1079The restoring coefficient $\gamma$ is a three-dimensional array read in during the \rou{tra\_dmp\_init} routine. The file name is specified by the namelist variable \np{cn\_resto}. The DMP\_TOOLS tool is provided to allow users to generate the netcdf file. 
    10821081The two main cases in which \eqref{Eq_tra_dmp} is used are \textit{(a)}  
    10921091diagnostic method \citep{Sarmiento1982}. It allows us to find the velocity  
    10931092field consistent with the model dynamics whilst having a $T$, $S$ field  
    1094 close to a given climatological field ($T_o$, $S_o$). The time scale  
    1095 associated with $S_o$ is generally not a constant but spatially varying  
    1096 in order to respect other properties. For example, it is usually set to zero  
    1097 in the mixed layer (defined either on a density or $S_o$ criterion)  
    1098 \citep{Madec_al_JPO96} and in the equatorial region  
    1099 \citep{Reverdin1991, Fujio1991, Marti_PhD92} since these two regions  
    1100 have a short time scale of adjustment; while smaller $\gamma$ are used  
    1101 in the deep ocean where the typical time scale is long \citep{Sarmiento1982}.  
    1102 In addition the time scale is reduced (even to zero) along the western  
    1103 boundary to allow the model to reconstruct its own western boundary  
    1104 structure in equilibrium with its physics.  
    1105 The choice of the shape of the Newtonian damping is controlled by two  
    1106 namelist parameters \np{nn\_hdmp} and \np{nn\_zdmp}. The former allows us to specify: the  
    1107 width of the equatorial band in which no damping is applied; a decrease  
    1108 in the vicinity of the coast; and a damping everywhere in the Red and Med Seas. 
    1109 The latter sets whether damping should act in the mixed layer or not.  
    1110 The time scale associated with the damping depends on the depth as 
    1111 a hyperbolic tangent, with \np{rn\_surf} as surface value, \np{rn\_bot} as  
    1112 bottom value and a transition depth of \np{rn\_dep}.   
     1093close to a given climatological field ($T_o$, $S_o$).  
    11141095The robust diagnostic method is very efficient in preventing temperature  
    11181099by stabilising the water column too much. 
    1120 An example of the computation of $\gamma$ for a robust diagnostic experiment  
    1121 with the ORCA2 model is provided in the \mdl{tradmp} module  
    1122 (subroutines \rou{dtacof} and \rou{cofdis} which compute the coefficient  
    1123 and the distance to the bathymetry, respectively). These routines are  
    1124 provided as examples and can be customised by the user.  
     1101The namelist parameter \np{nn\_zdmp} sets whether the damping should be applied in the whole water column or only below the mixed layer (defined either on a density or $S_o$ criterion). It is common to set the damping to zero in the mixed layer as the adjustment time scale is short here \citep{Madec_al_JPO96}. 
     1103\subsection[DMP\_TOOLS]{Generating resto.nc using DMP\_TOOLS} 
     1105DMP\_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. 
     1111\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. 
     1113The 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. 
     1115The 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}.   
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