Changeset 11512 for NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/NEMO/subfiles/annex_DOMAINcfg.tex
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- 2019-09-09T12:05:20+02:00 (5 years ago)
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NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/NEMO/subfiles/annex_DOMAINcfg.tex
r11353 r11512 8 8 \label{apdx:DOMAINcfg} 9 9 10 \ minitoc10 \chaptertoc 11 11 \vfill 12 12 \begin{figure}[b] … … 25 25 26 26 This tool will evolve into an independent utility with its own documentation but its 27 current manifestation is mostly a wrapper for \NEMO \forcode{DOM} modules more aligned to28 those in the previous versions of NEMO. These versions allowed the user to define some27 current manifestation is mostly a wrapper for \NEMO\ \forcode{DOM} modules more aligned to 28 those in the previous versions of \NEMO. These versions allowed the user to define some 29 29 horizontal and vertical grids through additional namelist parameters. Explanations of 30 30 these parameters are retained here for reference pending better documentation for … … 32 32 those read by \forcode{DOMAINcfg} via its own \forcode{namelist_ref} and 33 33 \forcode{namelist_cfg} files. Although, due to their origins, these namelists share names 34 with those used by NEMO, they are not interchangeable and should be considered independent34 with those used by \NEMO, they are not interchangeable and should be considered independent 35 35 of those described elsewhere in this manual. 36 36 … … 43 43 %--------------------------------------------namdom------------------------------------------------------- 44 44 45 \nlst{namdom_domcfg} 45 \nlst{namdom_domcfg} 46 46 %-------------------------------------------------------------------------------------------------------------- 47 47 48 48 The user has three options available in defining a horizontal grid, which involve the 49 namelist variable \np{jphgr\_mesh} of the \n gn{namdom} (\forcode{DOMAINcfg} variant only)49 namelist variable \np{jphgr\_mesh} of the \nam{dom} (\texttt{DOMAINcfg} variant only) 50 50 namelist. 51 51 … … 54 54 The coordinates and their first derivatives with respect to $i$ and $j$ are provided 55 55 in a input file (\ifile{coordinates}), read in \rou{hgr\_read} subroutine of the domhgr module. 56 This is now the only option available within \NEMO itself from v4.0 onwards.57 \item[\np{jphgr\_mesh}=1 to 5] A few simple analytical grids are provided (see below). 58 For other analytical grids, the \ textit{domhgr.f90} module (\forcode{DOMAINcfg} variant) must be59 modified by the user. In most cases, modifying the \mdl{usrdef\_hgr} module of \NEMO is60 a better alternative since this is designed to allow simple analytical domains to be 56 This is now the only option available within \NEMO\ itself from v4.0 onwards. 57 \item[\np{jphgr\_mesh}=1 to 5] A few simple analytical grids are provided (see below). 58 For other analytical grids, the \mdl{domhgr} module (\texttt{DOMAINcfg} variant) must be 59 modified by the user. In most cases, modifying the \mdl{usrdef\_hgr} module of \NEMO\ is 60 a better alternative since this is designed to allow simple analytical domains to be 61 61 configured and used without the need for external data files. 62 62 \end{description} 63 63 64 There are two simple cases of geographical grids on the sphere. With 65 \np{jphgr\_mesh}=1, the grid (expressed in degrees) is regular in space, 66 with grid sizes specified by parameters \np{ppe1\_deg} and \np{ppe2\_deg}, 67 respectively. Such a geographical grid can be very anisotropic at high latitudes 68 because of the convergence of meridians (the zonal scale factors $e_1$ 69 become much smaller than the meridional scale factors $e_2$). The Mercator 70 grid (\np{jphgr\_mesh}=4) avoids this anisotropy by refining the meridional scale 71 factors in the same way as the zonal ones. In this case, meridional scale factors 72 and latitudes are calculated analytically using the formulae appropriate for 73 a Mercator projection, based on \np{ppe1\_deg} which is a reference grid spacing 74 at the equator (this applies even when the geographical equator is situated outside 75 the model domain). 76 77 In these two cases (\np{jphgr\_mesh}=1 or 4), the grid position is defined by the 78 longitude and latitude of the south-westernmost point (\np{ppglamt0} 79 and \np{ppgphi0}). Note that for the Mercator grid the user need only provide 80 an approximate starting latitude: the real latitude will be recalculated analytically, 81 in order to ensure that the equator corresponds to line passing through $t$- 82 and $u$-points. 83 84 Rectangular grids ignoring the spherical geometry are defined with 85 \np{jphgr\_mesh} = 2, 3, 5. The domain is either an $f$-plane (\np{jphgr\_mesh} = 2, 86 Coriolis factor is constant) or a beta-plane (\np{jphgr\_mesh} = 3, the Coriolis factor 87 is linear in the $j$-direction). The grid size is uniform in meter in each direction, 88 and given by the parameters \np{ppe1\_m} and \np{ppe2\_m} respectively. 89 The zonal grid coordinate (\textit{glam} arrays) is in kilometers, starting at zero 90 with the first $t$-point. The meridional coordinate (gphi. arrays) is in kilometers, 91 and the second $t$-point corresponds to coordinate $gphit=0$. The input 92 variable \np{ppglam0} is ignored. \np{ppgphi0} is used to set the reference 93 latitude for computation of the Coriolis parameter. In the case of the beta plane, 94 \np{ppgphi0} corresponds to the center of the domain. Finally, the special case 95 \np{jphgr\_mesh}=5 corresponds to a beta plane in a rotated domain for the 96 GYRE configuration, representing a classical mid-latitude double gyre system. 97 The rotation allows us to maximize the jet length relative to the gyre areas 98 (and the number of grid points). 64 There are two simple cases of geographical grids on the sphere. With 65 \np{jphgr\_mesh}=1, the grid (expressed in degrees) is regular in space, 66 with grid sizes specified by parameters \np{ppe1\_deg} and \np{ppe2\_deg}, 67 respectively. Such a geographical grid can be very anisotropic at high latitudes 68 because of the convergence of meridians (the zonal scale factors $e_1$ 69 become much smaller than the meridional scale factors $e_2$). The Mercator 70 grid (\np{jphgr\_mesh}=4) avoids this anisotropy by refining the meridional scale 71 factors in the same way as the zonal ones. In this case, meridional scale factors 72 and latitudes are calculated analytically using the formulae appropriate for 73 a Mercator projection, based on \np{ppe1\_deg} which is a reference grid spacing 74 at the equator (this applies even when the geographical equator is situated outside 75 the model domain). 76 77 In these two cases (\np{jphgr\_mesh}=1 or 4), the grid position is defined by the 78 longitude and latitude of the south-westernmost point (\np{ppglamt0} 79 and \np{ppgphi0}). Note that for the Mercator grid the user need only provide 80 an approximate starting latitude: the real latitude will be recalculated analytically, 81 in order to ensure that the equator corresponds to line passing through $t$- 82 and $u$-points. 83 84 Rectangular grids ignoring the spherical geometry are defined with 85 \np{jphgr\_mesh} = 2, 3, 5. The domain is either an $f$-plane (\np{jphgr\_mesh} = 2, 86 Coriolis factor is constant) or a beta-plane (\np{jphgr\_mesh} = 3, the Coriolis factor 87 is linear in the $j$-direction). The grid size is uniform in meter in each direction, 88 and given by the parameters \np{ppe1\_m} and \np{ppe2\_m} respectively. 89 The zonal grid coordinate (\textit{glam} arrays) is in kilometers, starting at zero 90 with the first $t$-point. The meridional coordinate (gphi. arrays) is in kilometers, 91 and the second $t$-point corresponds to coordinate $gphit=0$. The input 92 variable \np{ppglam0} is ignored. \np{ppgphi0} is used to set the reference 93 latitude for computation of the Coriolis parameter. In the case of the beta plane, 94 \np{ppgphi0} corresponds to the center of the domain. Finally, the special case 95 \np{jphgr\_mesh}=5 corresponds to a beta plane in a rotated domain for the 96 GYRE configuration, representing a classical mid-latitude double gyre system. 97 The rotation allows us to maximize the jet length relative to the gyre areas 98 (and the number of grid points). 99 99 100 100 % ------------------------------------------------------------------------------------------------------------- … … 128 128 the vertical scale factors. The user must provide the analytical expression of both $z_0$ 129 129 and its first derivative with respect to $k$. This is done in routine \mdl{domzgr} 130 through statement functions, using parameters provided in the \n gn{namdom} namelist131 (\ forcode{DOMAINcfg} variant).130 through statement functions, using parameters provided in the \nam{dom} namelist 131 (\texttt{DOMAINcfg} variant). 132 132 133 133 It is possible to define a simple regular vertical grid by giving zero stretching … … 156 156 \begin{split} 157 157 z_0 (k) = h_{sur} - h_0 \; k &- \; h_1 \; \log \big[ \cosh ((k - h_{th}) / h_{cr}) \big] \\ 158 \; &- \; h2_1 \; \log \big[ \cosh ((k - h2_{th}) / h2_{cr}) \big] 158 \; &- \; h2_1 \; \log \big[ \cosh ((k - h2_{th}) / h2_{cr}) \big] 159 159 \end{split} 160 160 \end{gather} … … 177 177 \end{equation} 178 178 179 This formulation decreases the self-generated circulation into the ice shelf cavity 179 This formulation decreases the self-generated circulation into the ice shelf cavity 180 180 (which can, in extreme case, leads to numerical instability). This is now the recommended formulation for all configurations using v4.0 onwards. The analytical derivation of thicknesses is maintained for backwards compatibility. 181 181 … … 200 200 The resulting depths and scale factors as a function of the model levels are shown in 201 201 \autoref{fig:DOMCFG_zgr} and given in \autoref{tab:DOMCFG_orca_zgr}. 202 Those values correspond to the parameters \np{ppsur}, \np{ppa0}, \np{ppa1}, \np{ppkth} in \n gn{namcfg} namelist.202 Those values correspond to the parameters \np{ppsur}, \np{ppa0}, \np{ppa1}, \np{ppkth} in \nam{cfg} namelist. 203 203 204 204 Rather than entering parameters $h_{sur}$, $h_0$, and $h_1$ directly, it is possible to 205 205 recalculate them. In that case the user sets \np{ppsur}~$=$~\np{ppa0}~$=$~\np{ppa1}~$= 206 999999$., in \n gn{namcfg} namelist, and specifies instead the four following parameters:206 999999$., in \nam{cfg} namelist, and specifies instead the four following parameters: 207 207 \begin{itemize} 208 208 \item … … 309 309 310 310 Three options are possible for defining the bathymetry, according to the namelist variable 311 \np{nn\_bathy} (found in \n gn{namdom} namelist (\forcode{DOMAINCFG} variant) ):311 \np{nn\_bathy} (found in \nam{dom} namelist (\texttt{DOMAINCFG} variant) ): 312 312 \begin{description} 313 313 \item[\np{nn\_bathy}\forcode{ = 0}]: … … 322 322 The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters) at 323 323 each grid point of the model grid. 324 The bathymetry is usually built by interpolating a standard bathymetry product (\eg ETOPO2) onto324 The bathymetry is usually built by interpolating a standard bathymetry product (\eg\ ETOPO2) onto 325 325 the horizontal ocean mesh. 326 326 Defining the bathymetry also defines the coastline: where the bathymetry is zero, … … 352 352 \end{description} 353 353 %%% 354 354 355 355 % ------------------------------------------------------------------------------------------------------------- 356 356 % z-coordinate with constant thickness … … 386 386 thickness than $e_{3t}(jpk)$: the maximum thickness allowed is $2*e_{3t}(jpk - 1)$. 387 387 388 This has to be kept in mind when specifying values in \n gn{namdom} namelist389 (\ forcode{DOMMAINCFG} variant), such as the maximum depth \np{pphmax} in partial steps.388 This has to be kept in mind when specifying values in \nam{dom} namelist 389 (\texttt{DOMAINCFG} variant), such as the maximum depth \np{pphmax} in partial steps. 390 390 391 391 For example, with \np{pphmax}~$= 5750~m$ for the DRAKKAR 45 layer grid, the maximum ocean … … 405 405 %------------------------------------------nam_zgr_sco--------------------------------------------------- 406 406 % 407 \nlst{namzgr_sco_domcfg} 407 \nlst{namzgr_sco_domcfg} 408 408 %-------------------------------------------------------------------------------------------------------------- 409 Options are defined in \n gn{namzgr\_sco} (\forcode{DOMAINcfg} only).409 Options are defined in \nam{zgr\_sco} (\texttt{DOMAINcfg} only). 410 410 In $s$-coordinate (\np{ln\_sco}\forcode{ = .true.}), the depth and thickness of the model levels are defined from 411 411 the product of a depth field and either a stretching function or its derivative, respectively: … … 430 430 but care must be taken to ensure that the vertical stretch used is appropriate for the application. 431 431 432 The original default NEMOs-coordinate stretching is available if neither of the other options are specified as true432 The original default \NEMO\ s-coordinate stretching is available if neither of the other options are specified as true 433 433 (\np{ln\_s\_SH94}\forcode{ = .false.} and \np{ln\_s\_SF12}\forcode{ = .false.}). 434 434 This uses a depth independent $\tanh$ function for the stretching \citep{madec.delecluse.ea_JPO96}: … … 555 555 \label{subsec:DOMCFG_zgr_star} 556 556 557 This option is described in the Report by Levier \textit{et al.} (2007), available on the \NEMO web site.557 This option is described in the Report by Levier \textit{et al.} (2007), available on the \NEMO\ web site. 558 558 559 559 \biblio
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