Changeset 9389 for branches/2017/dev_merge_2017/DOC/tex_sub/chap_DOM.tex
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branches/2017/dev_merge_2017/DOC/tex_sub/chap_DOM.tex
r9388 r9389 1 \documentclass[ NEMO_book]{subfiles}1 \documentclass[../tex_main/NEMO_manual]{subfiles} 2 2 \begin{document} 3 3 % ================================================================ … … 309 309 ie1e2u\_v is a flag to flag set u and v surfaces are neither read nor computed.\\ 310 310 311 These fields can be read in an domain input file which name is setted in \np{cn \_domcfg} parameter specified in \ngn{namcfg}.311 These fields can be read in an domain input file which name is setted in \np{cn_domcfg} parameter specified in \ngn{namcfg}. 312 312 \forfile{../namelists/namcfg} 313 313 or they can be defined in an analytical way in MY\_SRC directory of the configuration. … … 413 413 414 414 All the arrays relating to a particular ocean model configuration (grid-point 415 position, scale factors, masks) can be saved in files if $ \np{nn\_msh}\not= 0$415 position, scale factors, masks) can be saved in files if $nn\_msh \not= 0$ 416 416 (namelist variable in \ngn{namdom}). This can be particularly useful for plots and off-line 417 417 diagnostics. In some cases, the user may choose to make a local modification … … 420 420 happens to be too wide due to insufficient model resolution). An example 421 421 is Gibraltar Strait in the ORCA2 configuration. When such modifications are done, 422 the output grid written when $ \np{nn\_msh} \not=0$ is no more equal to the input grid.422 the output grid written when $nn\_msh \not= 0$ is no more equal to the input grid. 423 423 424 424 $\ $\newline % force a new line … … 454 454 (d) hybrid $s-z$ coordinate, 455 455 (e) hybrid $s-z$ coordinate with partial step, and 456 (f) same as (e) but in the non-linear free surface (\protect\np{ln \_linssh}=false).456 (f) same as (e) but in the non-linear free surface (\protect\np{ln_linssh}=false). 457 457 Note that the non-linear free surface can be used with any of the 458 458 5 coordinates (a) to (e).} … … 464 464 option which can be enabled or disabled in the middle of an experiment. Three main 465 465 choices are offered (Fig.~\ref{Fig_z_zps_s_sps}a to c): $z$-coordinate with full step 466 bathymetry (\np{ln \_zco}~=~true), $z$-coordinate with partial step bathymetry467 (\np{ln \_zps}~=~true), or generalized, $s$-coordinate (\np{ln\_sco}~=~true).466 bathymetry (\np{ln_zco}~=~true), $z$-coordinate with partial step bathymetry 467 (\np{ln_zps}~=~true), or generalized, $s$-coordinate (\np{ln_sco}~=~true). 468 468 Hybridation of the three main coordinates are available: $s-z$ or $s-zps$ coordinate 469 469 (Fig.~\ref{Fig_z_zps_s_sps}d and \ref{Fig_z_zps_s_sps}e). By default a non-linear free surface is used: 470 470 the coordinate follow the time-variation of the free surface so that the transformation is time dependent: 471 $z(i,j,k,t)$ (Fig.~\ref{Fig_z_zps_s_sps}f). When a linear free surface is assumed (\np{ln \_linssh}=true),471 $z(i,j,k,t)$ (Fig.~\ref{Fig_z_zps_s_sps}f). When a linear free surface is assumed (\np{ln_linssh}=true), 472 472 the vertical coordinate are fixed in time, but the seawater can move up and down across the z=0 surface 473 473 (in other words, the top of the ocean in not a rigid-lid). 474 474 The last choice in terms of vertical coordinate concerns the presence (or not) in the model domain 475 of ocean cavities beneath ice shelves. Setting \np{ln \_isfcav} to true allows to manage ocean cavities,475 of ocean cavities beneath ice shelves. Setting \np{ln_isfcav} to true allows to manage ocean cavities, 476 476 otherwise they are filled in. This option is currently only available in $z$- or $zps$-coordinate, 477 477 and partial step are also applied at the ocean/ice shelf interface. … … 483 483 \ifile{bathy\_meter} file, so that the computation of the number of wet ocean point 484 484 in each water column is by-passed}. 485 If \np{ln \_isfcav}~=~true, an extra file input file describing the ice shelf draft485 If \np{ln_isfcav}~=~true, an extra file input file describing the ice shelf draft 486 486 (in meters) (\ifile{isf\_draft\_meter}) is needed. 487 487 … … 503 503 %%% 504 504 505 Unless a linear free surface is used (\np{ln \_linssh}=false), the arrays describing505 Unless a linear free surface is used (\np{ln_linssh}=false), the arrays describing 506 506 the grid point depths and vertical scale factors are three set of three dimensional arrays $(i,j,k)$ 507 507 defined at \textit{before}, \textit{now} and \textit{after} time step. The time at which they are 508 508 defined is indicated by a suffix:$\_b$, $\_n$, or $\_a$, respectively. They are updated at each model time step 509 509 using a fixed reference coordinate system which computer names have a $\_0$ suffix. 510 When the linear free surface option is used (\np{ln \_linssh}=true), \textit{before}, \textit{now}510 When the linear free surface option is used (\np{ln_linssh}=true), \textit{before}, \textit{now} 511 511 and \textit{after} arrays are simply set one for all to their reference counterpart. 512 512 … … 519 519 520 520 Three options are possible for defining the bathymetry, according to the 521 namelist variable \np{nn \_bathy} (found in \ngn{namdom} namelist):521 namelist variable \np{nn_bathy} (found in \ngn{namdom} namelist): 522 522 \begin{description} 523 \item[\np{nn \_bathy} = 0] a flat-bottom domain is defined. The total depth $z_w (jpk)$523 \item[\np{nn_bathy} = 0] a flat-bottom domain is defined. The total depth $z_w (jpk)$ 524 524 is given by the coordinate transformation. The domain can either be a closed 525 525 basin or a periodic channel depending on the parameter \np{jperio}. 526 \item[\np{nn \_bathy} = -1] a domain with a bump of topography one third of the526 \item[\np{nn_bathy} = -1] a domain with a bump of topography one third of the 527 527 domain width at the central latitude. This is meant for the "EEL-R5" configuration, 528 528 a periodic or open boundary channel with a seamount. 529 \item[\np{nn \_bathy} = 1] read a bathymetry and ice shelf draft (if needed).529 \item[\np{nn_bathy} = 1] read a bathymetry and ice shelf draft (if needed). 530 530 The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters) 531 531 at each grid point of the model grid. The bathymetry is usually built by interpolating a standard bathymetry product … … 535 535 536 536 The \ifile{isfdraft\_meter} file (Netcdf format) provides the ice shelf draft (positive, in meters) 537 at each grid point of the model grid. This file is only needed if \np{ln \_isfcav}~=~true.537 at each grid point of the model grid. This file is only needed if \np{ln_isfcav}~=~true. 538 538 Defining the ice shelf draft will also define the ice shelf edge and the grounding line position. 539 539 \end{description} … … 550 550 % z-coordinate and reference coordinate transformation 551 551 % ------------------------------------------------------------------------------------------------------------- 552 \subsection[$z$-coordinate (\protect\np{ln \_zco}]553 {$z$-coordinate (\protect\np{ln \_zco}=true) and reference coordinate}552 \subsection[$z$-coordinate (\protect\np{ln_zco}] 553 {$z$-coordinate (\protect\np{ln_zco}=true) and reference coordinate} 554 554 \label{DOM_zco} 555 555 … … 593 593 (Fig.~\ref{Fig_zgr}). 594 594 595 If the ice shelf cavities are opened (\np{ln \_isfcav}=~true~), the definition of $z_0$ is the same.595 If the ice shelf cavities are opened (\np{ln_isfcav}=~true~), the definition of $z_0$ is the same. 596 596 However, definition of $e_3^0$ at $t$- and $w$-points is respectively changed to: 597 597 \begin{equation} \label{DOM_zgr_ana} … … 688 688 % z-coordinate with partial step 689 689 % ------------------------------------------------------------------------------------------------------------- 690 \subsection [$z$-coordinate with partial step (\protect\np{ln \_zps})]691 {$z$-coordinate with partial step (\protect\np{ln \_zps}=.true.)}690 \subsection [$z$-coordinate with partial step (\protect\np{ln_zps})] 691 {$z$-coordinate with partial step (\protect\np{ln_zps}=.true.)} 692 692 \label{DOM_zps} 693 693 %--------------------------------------------namdom------------------------------------------------------- … … 712 712 Two variables in the namdom namelist are used to define the partial step 713 713 vertical grid. The mimimum water thickness (in meters) allowed for a cell 714 partially filled with bathymetry at level jk is the minimum of \np{rn \_e3zps\_min}715 (thickness in meters, usually $20~m$) or $e_{3t}(jk)* \np{rn\_e3zps\_rat}$ (a fraction,714 partially filled with bathymetry at level jk is the minimum of \np{rn_e3zps_min} 715 (thickness in meters, usually $20~m$) or $e_{3t}(jk)*rn\_e3zps\_rat$ (a fraction, 716 716 usually 10\%, of the default thickness $e_{3t}(jk)$). 717 717 … … 721 721 % s-coordinate 722 722 % ------------------------------------------------------------------------------------------------------------- 723 \subsection [$s$-coordinate (\protect\np{ln \_sco})]724 {$s$-coordinate (\protect\np{ln \_sco}=true)}723 \subsection [$s$-coordinate (\protect\np{ln_sco})] 724 {$s$-coordinate (\protect\np{ln_sco}=true)} 725 725 \label{DOM_sco} 726 726 %------------------------------------------nam_zgr_sco--------------------------------------------------- … … 728 728 %-------------------------------------------------------------------------------------------------------------- 729 729 Options are defined in \ngn{namzgr\_sco}. 730 In $s$-coordinate (\np{ln \_sco}~=~true), the depth and thickness of the model730 In $s$-coordinate (\np{ln_sco}~=~true), the depth and thickness of the model 731 731 levels are defined from the product of a depth field and either a stretching 732 732 function or its derivative, respectively: … … 744 744 depth, since a mixed step-like and bottom-following representation of the 745 745 topography can be used (Fig.~\ref{Fig_z_zps_s_sps}d-e) or an envelop bathymetry can be defined (Fig.~\ref{Fig_z_zps_s_sps}f). 746 The namelist parameter \np{rn \_rmax} determines the slope at which the terrain-following coordinate intersects746 The namelist parameter \np{rn_rmax} determines the slope at which the terrain-following coordinate intersects 747 747 the sea bed and becomes a pseudo z-coordinate. 748 The coordinate can also be hybridised by specifying \np{rn \_sbot\_min} and \np{rn\_sbot\_max}748 The coordinate can also be hybridised by specifying \np{rn_sbot_min} and \np{rn_sbot_max} 749 749 as the minimum and maximum depths at which the terrain-following vertical coordinate is calculated. 750 750 … … 753 753 754 754 The original default NEMO s-coordinate stretching is available if neither of the other options 755 are specified as true (\np{ln \_s\_SH94}~=~false and \np{ln\_s\_SF12}~=~false).755 are specified as true (\np{ln_s_SH94}~=~false and \np{ln_s_SF12}~=~false). 756 756 This uses a depth independent $\tanh$ function for the stretching \citep{Madec_al_JPO96}: 757 757 … … 779 779 780 780 A stretching function, modified from the commonly used \citet{Song_Haidvogel_JCP94} 781 stretching (\np{ln \_s\_SH94}~=~true), is also available and is more commonly used for shelf seas modelling:781 stretching (\np{ln_s_SH94}~=~true), is also available and is more commonly used for shelf seas modelling: 782 782 783 783 \begin{equation} … … 796 796 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 797 797 798 where $H_c$ is the critical depth (\np{rn \_hc}) at which the coordinate transitions from799 pure $\sigma$ to the stretched coordinate, and $\theta$ (\np{rn \_theta}) and $b$ (\np{rn\_bb})798 where $H_c$ is the critical depth (\np{rn_hc}) at which the coordinate transitions from 799 pure $\sigma$ to the stretched coordinate, and $\theta$ (\np{rn_theta}) and $b$ (\np{rn_bb}) 800 800 are the surface and bottom control parameters such that $0\leqslant \theta \leqslant 20$, and 801 801 $0\leqslant b\leqslant 1$. $b$ has been designed to allow surface and/or bottom 802 802 increase of the vertical resolution (Fig.~\ref{Fig_sco_function}). 803 803 804 Another example has been provided at version 3.5 (\np{ln \_s\_SF12}) that allows804 Another example has been provided at version 3.5 (\np{ln_s_SF12}) that allows 805 805 a fixed surface resolution in an analytical terrain-following stretching \citet{Siddorn_Furner_OM12}. 806 806 In this case the a stretching function $\gamma$ is defined such that: … … 823 823 824 824 This gives an analytical stretching of $\sigma$ that is solvable in $A$ and $B$ as a function of 825 the user prescribed stretching parameter $\alpha$ (\np{rn \_alpha}) that stretches towards826 the surface ($\alpha > 1.0$) or the bottom ($\alpha < 1.0$) and user prescribed surface (\np{rn \_zs})825 the user prescribed stretching parameter $\alpha$ (\np{rn_alpha}) that stretches towards 826 the surface ($\alpha > 1.0$) or the bottom ($\alpha < 1.0$) and user prescribed surface (\np{rn_zs}) 827 827 and bottom depths. The bottom cell depth in this example is given as a function of water depth: 828 828 … … 831 831 \end{equation} 832 832 833 where the namelist parameters \np{rn \_zb\_a} and \np{rn\_zb\_b} are $a$ and $b$ respectively.833 where the namelist parameters \np{rn_zb_a} and \np{rn_zb_b} are $a$ and $b$ respectively. 834 834 835 835 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> … … 843 843 This gives a smooth analytical stretching in computational space that is constrained to given specified surface and bottom grid cell thicknesses in real space. This is not to be confused with the hybrid schemes that superimpose geopotential coordinates on terrain following coordinates thus creating a non-analytical vertical coordinate that therefore may suffer from large gradients in the vertical resolutions. This stretching is less straightforward to implement than the \citet{Song_Haidvogel_JCP94} stretching, but has the advantage of resolving diurnal processes in deep water and has generally flatter slopes. 844 844 845 As with the \citet{Song_Haidvogel_JCP94} stretching the stretch is only applied at depths greater than the critical depth $h_c$. In this example two options are available in depths shallower than $h_c$, with pure sigma being applied if the \np{ln \_sigcrit} is true and pure z-coordinates if it is false (the z-coordinate being equal to the depths of the stretched coordinate at $h_c$.845 As with the \citet{Song_Haidvogel_JCP94} stretching the stretch is only applied at depths greater than the critical depth $h_c$. In this example two options are available in depths shallower than $h_c$, with pure sigma being applied if the \np{ln_sigcrit} is true and pure z-coordinates if it is false (the z-coordinate being equal to the depths of the stretched coordinate at $h_c$. 846 846 847 847 Minimising the horizontal slope of the vertical coordinate is important in terrain-following systems as large slopes lead to hydrostatic consistency. A hydrostatic consistency parameter diagnostic following \citet{Haney1991} has been implemented, and is output as part of the model mesh file at the start of the run. … … 850 850 % z*- or s*-coordinate 851 851 % ------------------------------------------------------------------------------------------------------------- 852 \subsection{$z^*$- or $s^*$-coordinate (\protect\np{ln \_linssh}=false) }852 \subsection{$z^*$- or $s^*$-coordinate (\protect\np{ln_linssh}=false) } 853 853 \label{DOM_zgr_star} 854 854 … … 881 881 In case of ice shelf cavities, modifications of the model bathymetry and ice shelf draft into 882 882 the cavities are performed in the \textit{zgr\_isf} routine. The compatibility between ice shelf draft and bathymetry is checked. 883 All the locations where the isf cavity is thinnest than \np{rn \_isfhmin} meters are grounded ($i.e.$ masked).883 All the locations where the isf cavity is thinnest than \np{rn_isfhmin} meters are grounded ($i.e.$ masked). 884 884 If only one cell on the water column is opened at $t$-, $u$- or $v$-points, the bathymetry or the ice shelf draft is dug to fit this constrain. 885 885 If the incompatibility is too strong (need to dig more than 1 cell), the cell is masked.\\ … … 921 921 Options are defined in \ngn{namtsd}. 922 922 By default, the ocean start from rest (the velocity field is set to zero) and the initialization of 923 temperature and salinity fields is controlled through the \np{ln \_tsd\_ini} namelist parameter.923 temperature and salinity fields is controlled through the \np{ln_tsd_ini} namelist parameter. 924 924 \begin{description} 925 925 \item[ln\_tsd\_init = .true.] use a T and S input files that can be given on the model grid itself or 926 926 on their native input data grid. In the latter case, the data will be interpolated on-the-fly both in the 927 927 horizontal and the vertical to the model grid (see \S~\ref{SBC_iof}). The information relative to the 928 input files are given in the \np{sn \_tem} and \np{sn\_sal} structures.928 input files are given in the \np{sn_tem} and \np{sn_sal} structures. 929 929 The computation is done in the \mdl{dtatsd} module. 930 930 \item[ln\_tsd\_init = .false.] use constant salinity value of 35.5 psu and an analytical profile of temperature
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