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branches/2012/dev_MERGE_2012/DOC/TexFiles/Chapters/Chap_DOM.tex
r3294 r3680 502 502 time-variation of the free surface so that the transformation is time dependent: 503 503 $z(i,j,k,t)$ (Fig.~\ref{Fig_z_zps_s_sps}f). This option can be used with full step 504 bathymetry or $s$-coordinate (hybrid eand partial step coordinates have not504 bathymetry or $s$-coordinate (hybrid and partial step coordinates have not 505 505 yet been tested in NEMO v2.3). 506 506 … … 743 743 levels are defined from the product of a depth field and either a stretching 744 744 function or its derivative, respectively: 745 745 746 \begin{equation} \label{DOM_sco_ana} 746 747 \begin{split} … … 749 750 \end{split} 750 751 \end{equation} 752 751 753 where $h$ is the depth of the last $w$-level ($z_0(k)$) defined at the $t$-point 752 754 location in the horizontal and $z_0(k)$ is a function which varies from $0$ at the sea 753 755 surface to $1$ at the ocean bottom. The depth field $h$ is not necessary the ocean 754 756 depth, since a mixed step-like and bottom-following representation of the 755 topography can be used (Fig.~\ref{Fig_z_zps_s_sps}d-e). In the example provided 756 (\rou{zgr\_sco} routine, see \mdl{domzgr}) $h$ is a smooth envelope bathymetry 757 and steps are used to represent sharp bathymetric gradients. 758 759 A new flexible stretching function, modified from \citet{Song_Haidvogel_JCP94} is provided as an example: 757 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). 758 The namelist parameter \np{rn\_rmax} determines the slope at which the terrain-following coordinate intersects the sea bed and becomes a pseudo z-coordinate. The coordinate can also be hybridised by specifying \np{rn\_sbot\_min} and \np{rn\_sbot\_max} as the minimum and maximum depths at which the terrain-following vertical coordinate is calculated. 759 760 Options for stretching the coordinate are provided as examples, but care must be taken to ensure that the vertical stretch used is appropriate for the application. 761 762 The original default NEMO s-coordinate stretching is available if neither of the other options are specified as true (\np{ln\_sco\_SH94}~=~false and \np{ln\_sco\_SF12}~=~false.) This uses a depth independent $\tanh$ function for the stretching \citep{Madec_al_JPO96}: 763 764 \begin{equation} 765 z = s_{min}+C\left(s\right)\left(H-s_{min}\right) 766 \label{eq:SH94_1} 767 \end{equation} 768 769 where $s_{min}$ is the depth at which the s-coordinate stretching starts and allows a z-coordinate to placed on top of the stretched coordinate, and z is the depth (negative down from the asea surface). 770 771 \begin{equation} 772 s = -\frac{k}{n-1} \quad \text{ and } \quad 0 \leq k \leq n-1 773 \label{eq:s} 774 \end{equation} 775 760 776 \begin{equation} \label{DOM_sco_function} 761 777 \begin{split} 762 z &= h_c +( h-h_c)\;c s) \\ 763 c(s) &= \frac{ \left[ \tanh{ \left( \theta \, (s+b) \right)} 778 C(s) &= \frac{ \left[ \tanh{ \left( \theta \, (s+b) \right)} 764 779 - \tanh{ \left( \theta \, b \right)} \right]} 765 780 {2\;\sinh \left( \theta \right)} 766 781 \end{split} 767 782 \end{equation} 768 where $h_c$ is the thermocline depth and $\theta$ and $b$ are the surface and 783 784 A stretching function, modified from the commonly used \citet{Song_Haidvogel_JCP94} stretching (\np{ln\_sco\_SH94}~=~true), is also available and is more commonly used for shelf seas modelling: 785 786 \begin{equation} 787 C\left(s\right) = \left(1 - b \right)\frac{ \sinh\left( \theta s\right)}{\sinh\left(\theta\right)} + \\ 788 b\frac{ \tanh \left[ \theta \left(s + \frac{1}{2} \right)\right] - \tanh\left(\frac{\theta}{2}\right)}{ 2\tanh\left (\frac{\theta}{2}\right)} 789 \label{eq:SH94_2} 790 \end{equation} 791 792 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 793 \begin{figure}[!ht] \begin{center} 794 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_sco_function.pdf} 795 \caption{ \label{Fig_sco_function} 796 Examples of the stretching function applied to a seamount; from left to right: 797 surface, surface and bottom, and bottom intensified resolutions} 798 \end{center} \end{figure} 799 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 800 801 where $H_c$ is the critical depth (\np{rn\_hc}) at which the coordinate transitions from pure $\sigma$ to the stretched coordinate, and $\theta$ (\np{rn\_theta}) and $b$ (\np{rn\_bb}) are the surface and 769 802 bottom control parameters such that $0\leqslant \theta \leqslant 20$, and 770 803 $0\leqslant b\leqslant 1$. $b$ has been designed to allow surface and/or bottom 771 804 increase of the vertical resolution (Fig.~\ref{Fig_sco_function}). 772 805 773 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 774 \begin{figure}[!tb] \begin{center} 775 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_sco_function.pdf} 776 \caption{ \label{Fig_sco_function} 777 Examples of the stretching function applied to a sea mont; from left to right: 778 surface, surface and bottom, and bottom intensified resolutions} 779 \end{center} \end{figure} 780 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 806 Another example has been provided at version 3.5 (\np{ln\_sco\_SF12}) that allows a fixed surface resolution in an analytical terrain-following stretching \citet{Siddorn_Furner_OM12}. In this case the a stretching function $\gamma$ is defined such that: 807 808 \begin{equation} 809 z = -\gamma h \quad \text{ with } \quad 0 \leq \gamma \leq 1 810 \label{eq:z} 811 \end{equation} 812 813 The function is defined with respect to $\sigma$, the unstretched terrain-following coordinate: 814 815 \begin{equation} \label{DOM_gamma_deriv} 816 \gamma= A\left(\sigma-\frac{1}{2}\left(\sigma^{2}+f\left(\sigma\right)\right)\right)+B\left(\sigma^{3}-f\left(\sigma\right)\right)+f\left(\sigma\right) 817 \end{equation} 818 819 Where: 820 \begin{equation} \label{DOM_gamma} 821 f\left(\sigma\right)=\left(\alpha+2\right)\sigma^{\alpha+1}-\left(\alpha+1\right)\sigma^{\alpha+2} \quad \text{ and } \quad \sigma = \frac{k}{n-1} 822 \end{equation} 823 824 This gives an analytical stretching of $\sigma$ that is solvable in $A$ and $B$ as a function of the user prescribed stretching parameter $\alpha$ (\np{rn\_alpha}) that stretches towards the surface ($\alpha > 1.0$) or the bottom ($\alpha < 1.0$) and user prescribed surface (\np{rn\_zs}) and bottom depths. The bottom cell depth in this example is given as a function of water depth: 825 826 \begin{equation} \label{DOM_zb} 827 Z_b= h a + b 828 \end{equation} 829 830 where the namelist parameters \np{rn\_zb\_a} and \np{rn\_zb\_b} are $a$ and $b$ respectively. 831 832 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 833 \begin{figure}[!ht] 834 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/FIG_DOM_compare_coordinates_surface.pdf} 835 \caption{A comparison of the \citet{Song_Haidvogel_JCP94} $S$-coordinate (solid lines), a 50 level $Z$-coordinate (contoured surfaces) and the \citet{Siddorn_Furner_OM12} $S$-coordinate (dashed lines) in the surface 100m for a idealised bathymetry that goes from 50m to 5500m depth. For clarity every third coordinate surface is shown.} 836 \label{fig_compare_coordinates_surface} 837 \end{figure} 838 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 839 840 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. 841 842 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 $h_c$. 843 844 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. 781 845 782 846 % -------------------------------------------------------------------------------------------------------------
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