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branches/DEV_r1826_DOC/DOC/TexFiles/Chapters/Chap_DOM.tex
r1831 r1843 14 14 % - daymod: definition of the time domain (nit000, nitend andd the calendar) 15 15 % -geo2ocean: how to switch from geographic to mesh coordinate 16 % - domclo: closed sea and lakes.... management of closea sea area : specific to global configuration, both forced and coupled16 % - domclo: closed sea and lakes.... management of closea sea area : specific to global configuration, both forced and coupled 17 17 18 18 \gmcomment{STEVEN :maybe a picture of the directory structure in the introduction … … 392 392 \begin{description} 393 393 \item[\jp{jphgr\_mesh}=0] The most general curvilinear orthogonal grids. 394 The coordinates and their first derivatives with respect to $i$ and $j$ are 395 provided in a file, read in \rou{hgr\_read} subroutine of the domhgr module.394 The coordinates and their first derivatives with respect to $i$ and $j$ are provided 395 in a input file (\ifile{coordinates}), read in \rou{hgr\_read} subroutine of the domhgr module. 396 396 \item[\jp{jphgr\_mesh}=1 to 5] A few simple analytical grids are provided (see below). 397 397 For other analytical grids, the \mdl{domhgr} module must be modified by the user. … … 442 442 % Grid files 443 443 % ------------------------------------------------------------------------------------------------------------- 444 \subsection{ Grid files}444 \subsection{Output Grid files} 445 445 \label{DOM_hgr_files} 446 446 … … 507 507 Contrary to the horizontal grid, the vertical grid is computed in the code and no 508 508 provision is made for reading it from a file. The only input file is the bathymetry 509 (in meters)\footnote{N.B. in full step $z$-coordinate, a \textit{bathy\_level} file can 510 replace the \textit{bathy\_meter} file, so that the computation of the number of 511 wet ocean point in each water column is by-passed}. After reading the bathymetry, 512 the algorithm for vertical grid definition differs between the different options: 509 (in meters) (\ifile{bathy\_meter}) 510 \footnote{N.B. in full step $z$-coordinate, a \ifile{bathy\_level} file can replace the 511 \ifile{bathy\_meter} file, so that the computation of the number of wet ocean point 512 in each water column is by-passed}. 513 After reading the bathymetry, the algorithm for vertical grid definition differs 514 between the different options: 513 515 \begin{description} 514 516 \item[\textit{zco}] set a reference coordinate transformation $z_0 (k)$, and set $z(i,j,k,t)=z_0 (k)$. … … 553 555 domain width at the central latitude. This is meant for the "EEL-R5" configuration, 554 556 a periodic or open boundary channel with a seamount. 555 \item[\np{ntopo} = 1] read a bathymetry. The bathymetryfile (Netcdf format)557 \item[\np{ntopo} = 1] read a bathymetry. The \ifile{bathy\_meter} file (Netcdf format) 556 558 provides the ocean depth (positive, in meters) at each grid point of the model grid. 557 559 The bathymetry is usually built by interpolating a standard bathymetry product … … 560 562 (all levels are masked). 561 563 \end{description} 562 563 When using the rigid lid approximation (\key{dynspg\_rl} is defined) isolated land564 masses (islands) must be identified by negative integers in the input bathymetry file565 (see \S\ref{MISC_solisl}).566 564 567 565 When a global ocean is coupled to an atmospheric model it is better to represent … … 802 800 gives the number of ocean levels ($i.e.$ those that are not masked) at each 803 801 $t$-point. mbathy is computed from the meter bathymetry using the definiton of 804 gdept as the number of $t$-points which gdept $\leq$ bathy. Note that in version 805 NEMO v2.3, the user still has to provide the "level" bathymetry in a NetCDF 806 file when using the full step option (\np{ln\_zco}), rather than the bathymetry 807 in meters: both will be allowed in future versions. 802 gdept as the number of $t$-points which gdept $\leq$ bathy. 808 803 809 804 Modifications of the model bathymetry are performed in the \textit{bat\_ctl} 810 805 routine (see \mdl{domzgr} module) after mbathy is computed. Isolated grid points 811 806 that do not communicate with another ocean point at the same level are eliminated. 812 813 In the case of the rigid-lid approximation when islands occur in the computational814 domain (\np{ln\_dynspg\_rl}=.true. and \key{island} is defined), the \textit{mbathy}815 array must be provided and takes values from $-N$ to \jp{jpk}-1. It provides the816 following information: $mbathy(i,j) = -n, \ n \in \left] 0,N \right]$, $t$-points are817 land points on the $n^{th}$ island ; $mbathy(i,j) =0$, $t$-points are land points818 on the main land (continent) ; $mbathy(i,j) =k$, the first $k$ $t$- and $w$-points819 are ocean points, the others are points below the ocean floor.820 821 This is used to compute the island barotropic stream function used in the rigid lid822 computation (see \S\ref{MISC_solisl}).823 807 824 808 From the \textit{mbathy} array, the mask fields are defined as follows:
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