[707] | 1 | % ================================================================ |
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| 2 | % Chapter 1 Ñ Model Basics |
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| 3 | % ================================================================ |
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| 4 | |
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| 5 | \chapter{Model basics} |
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| 6 | \label{PE} |
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| 7 | \minitoc |
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| 8 | |
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| 9 | |
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[1831] | 10 | \newpage |
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| 11 | $\ $\newline % force a new ligne |
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| 12 | |
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[707] | 13 | % ================================================================ |
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| 14 | % Primitive Equations |
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| 15 | % ================================================================ |
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| 16 | \section{Primitive Equations} |
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| 17 | \label{PE_PE} |
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| 18 | |
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| 19 | % ------------------------------------------------------------------------------------------------------------- |
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| 20 | % Vector Invariant Formulation |
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| 21 | % ------------------------------------------------------------------------------------------------------------- |
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| 22 | |
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| 23 | \subsection{Vector Invariant Formulation} |
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| 24 | \label{PE_Vector} |
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| 25 | |
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| 26 | |
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[996] | 27 | The ocean is a fluid that can be described to a good approximation by the primitive |
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| 28 | equations, $i.e.$ the Navier-Stokes equations along with a nonlinear equation of |
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| 29 | state which couples the two active tracers (temperature and salinity) to the fluid |
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| 30 | velocity, plus the following additional assumptions made from scale considerations: |
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[707] | 31 | |
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[1224] | 32 | \textit{(1) spherical earth approximation: }the geopotential surfaces are assumed to |
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| 33 | be spheres so that gravity (local vertical) is parallel to the earth's radius |
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[707] | 34 | |
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| 35 | \textit{(2) thin-shell approximation: }the ocean depth is neglected compared to the earth's radius |
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| 36 | |
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[1224] | 37 | \textit{(3) turbulent closure hypothesis: }the turbulent fluxes (which represent the effect |
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| 38 | of small scale processes on the large-scale) are expressed in terms of large-scale features |
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[707] | 39 | |
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[1224] | 40 | \textit{(4) Boussinesq hypothesis:} density variations are neglected except in their |
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| 41 | contribution to the buoyancy force |
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[707] | 42 | |
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[1224] | 43 | \textit{(5) Hydrostatic hypothesis: }the vertical momentum equation is reduced to a |
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| 44 | balance between the vertical pressure gradient and the buoyancy force (this removes |
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| 45 | convective processes from the initial Navier-Stokes equations and so convective processes |
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| 46 | must be parameterized instead) |
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[707] | 47 | |
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[1224] | 48 | \textit{(6) Incompressibility hypothesis: }the three dimensional divergence of the velocity |
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| 49 | vector is assumed to be zero. |
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[707] | 50 | |
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[1224] | 51 | Because the gravitational force is so dominant in the equations of large-scale motions, |
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| 52 | it is useful to choose an orthogonal set of unit vectors (\textbf{i},\textbf{j},\textbf{k}) linked |
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| 53 | to the earth such that \textbf{k} is the local upward vector and (\textbf{i},\textbf{j}) are two |
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| 54 | vectors orthogonal to \textbf{k}, $i.e.$ tangent to the geopotential surfaces. Let us define |
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| 55 | the following variables: \textbf{U} the vector velocity, $\textbf{U}=\textbf{U}_h + w\, \textbf{k}$ |
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| 56 | (the subscript $h$ denotes the local horizontal vector, $i.e.$ over the (\textbf{i},\textbf{j}) plane), |
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| 57 | $T$ the potential temperature, $S$ the salinity, \textit{$\rho $} the \textit{in situ} density. |
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| 58 | The vector invariant form of the primitive equations in the (\textbf{i},\textbf{j},\textbf{k}) |
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| 59 | vector system provides the following six equations (namely the momentum balance, the |
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| 60 | hydrostatic equilibrium, the incompressibility equation, the heat and salt conservation |
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| 61 | equations and an equation of state): |
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[707] | 62 | \begin{subequations} \label{Eq_PE} |
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| 63 | \begin{equation} \label{Eq_PE_dyn} |
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| 64 | \frac{\partial {\rm {\bf U}}_h }{\partial t}= |
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| 65 | -\left[ {\left( {\nabla \times {\rm {\bf U}}} \right)\times {\rm {\bf U}} |
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| 66 | +\frac{1}{2}\nabla \left( {{\rm {\bf U}}^2} \right)} \right]_h |
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| 67 | -f\;{\rm {\bf k}}\times {\rm {\bf U}}_h |
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[817] | 68 | -\frac{1}{\rho _o }\nabla _h p + {\rm {\bf D}}^{\rm {\bf U}} + {\rm {\bf F}}^{\rm {\bf U}} |
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[707] | 69 | \end{equation} |
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| 70 | \begin{equation} \label{Eq_PE_hydrostatic} |
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| 71 | \frac{\partial p }{\partial z} = - \rho \ g |
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| 72 | \end{equation} |
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| 73 | \begin{equation} \label{Eq_PE_continuity} |
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| 74 | \nabla \cdot {\bf U}= 0 |
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| 75 | \end{equation} |
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| 76 | \begin{equation} \label{Eq_PE_tra_T} |
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[817] | 77 | \frac{\partial T}{\partial t} = - \nabla \cdot \left( T \ \rm{\bf U} \right) + D^T + F^T |
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[707] | 78 | \end{equation} |
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| 79 | \begin{equation} \label{Eq_PE_tra_S} |
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[817] | 80 | \frac{\partial S}{\partial t} = - \nabla \cdot \left( S \ \rm{\bf U} \right) + D^S + F^S |
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[707] | 81 | \end{equation} |
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| 82 | \begin{equation} \label{Eq_PE_eos} |
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| 83 | \rho = \rho \left( T,S,p \right) |
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| 84 | \end{equation} |
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| 85 | \end{subequations} |
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[1224] | 86 | where $\nabla$ is the generalised derivative vector operator in $(\bf i,\bf j, \bf k)$ directions, |
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| 87 | $t$ is the time, $z$ is the vertical coordinate, $\rho $ is the \textit{in situ} density given by |
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| 88 | the equation of state (\ref{Eq_PE_eos}), $\rho_o$ is a reference density, $p$ the pressure, |
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| 89 | $f=2 \bf \Omega \cdot \bf k$ is the Coriolis acceleration (where $\bf \Omega$ is the Earth's |
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| 90 | angular velocity vector), and $g$ is the gravitational acceleration. |
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| 91 | ${\rm {\bf D}}^{\rm {\bf U}}$, $D^T$ and $D^S$ are the parameterisations of small-scale |
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| 92 | physics for momentum, temperature and salinity, and ${\rm {\bf F}}^{\rm {\bf U}}$, $F^T$ |
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| 93 | and $F^S$ surface forcing terms. Their nature and formulation are discussed in |
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| 94 | \S\ref{PE_zdf_ldf} and page \S\ref{PE_boundary_condition}. |
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[707] | 95 | |
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| 96 | . |
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| 97 | |
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| 98 | % ------------------------------------------------------------------------------------------------------------- |
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| 99 | % Boundary condition |
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| 100 | % ------------------------------------------------------------------------------------------------------------- |
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| 101 | \subsection{Boundary Conditions} |
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| 102 | \label{PE_boundary_condition} |
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| 103 | |
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[1224] | 104 | An ocean is bounded by complex coastlines, bottom topography at its base and an air-sea |
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| 105 | or ice-sea interface at its top. These boundaries can be defined by two surfaces, $z=-H(i,j)$ |
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| 106 | and $z=\eta(i,j,k,t)$, where $H$ is the depth of the ocean bottom and $\eta$ is the height |
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| 107 | of the sea surface. Both $H$ and $\eta$ are usually referenced to a given surface, $z=0$, |
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| 108 | chosen as a mean sea surface (Fig.~\ref{Fig_ocean_bc}). Through these two boundaries, |
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| 109 | the ocean can exchange fluxes of heat, fresh water, salt, and momentum with the solid earth, |
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| 110 | the continental margins, the sea ice and the atmosphere. However, some of these fluxes are |
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| 111 | so weak that even on climatic time scales of thousands of years they can be neglected. |
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| 112 | In the following, we briefly review the fluxes exchanged at the interfaces between the ocean |
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| 113 | and the other components of the earth system. |
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[707] | 114 | |
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| 115 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 116 | \begin{figure}[!ht] \label{Fig_ocean_bc} \begin{center} |
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[998] | 117 | \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_I_ocean_bc.pdf} |
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[1224] | 118 | \caption{The ocean is bounded by two surfaces, $z=-H(i,j)$ and $z=\eta(i,j,k,t)$, where $H$ |
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| 119 | is the depth of the sea floor and $\eta$ the height of the sea surface. Both $H$ and $\eta $ |
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| 120 | are referenced to $z=0$.} |
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[707] | 121 | \end{center} \end{figure} |
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| 122 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 123 | |
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[817] | 124 | |
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[707] | 125 | \begin{description} |
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[1224] | 126 | \item[Land - ocean interface:] the major flux between continental margins and the ocean is |
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| 127 | a mass exchange of fresh water through river runoff. Such an exchange modifies the sea |
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| 128 | surface salinity especially in the vicinity of major river mouths. It can be neglected for short |
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| 129 | range integrations but has to be taken into account for long term integrations as it influences |
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| 130 | the characteristics of water masses formed (especially at high latitudes). It is required in order |
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| 131 | to close the water cycle of the climate system. It is usually specified as a fresh water flux at |
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| 132 | the air-sea interface in the vicinity of river mouths. |
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| 133 | \item[Solid earth - ocean interface:] heat and salt fluxes through the sea floor are small, |
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| 134 | except in special areas of little extent. They are usually neglected in the model |
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| 135 | \footnote{In fact, it has been shown that the heat flux associated with the solid Earth cooling |
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| 136 | ($i.e.$the geothermal heating) is not negligible for the thermohaline circulation of the world |
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| 137 | ocean (see \ref{TRA_bbc}).}. |
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| 138 | The boundary condition is thus set to no flux of heat and salt across solid boundaries. |
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| 139 | For momentum, the situation is different. There is no flow across solid boundaries, |
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| 140 | $i.e.$ the velocity normal to the ocean bottom and coastlines is zero (in other words, |
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| 141 | the bottom velocity is parallel to solid boundaries). This kinematic boundary condition |
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| 142 | can be expressed as: |
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[707] | 143 | \begin{equation} \label{Eq_PE_w_bbc} |
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| 144 | w = -{\rm {\bf U}}_h \cdot \nabla _h \left( H \right) |
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| 145 | \end{equation} |
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[1224] | 146 | In addition, the ocean exchanges momentum with the earth through frictional processes. |
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| 147 | Such momentum transfer occurs at small scales in a boundary layer. It must be parameterized |
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| 148 | in terms of turbulent fluxes using bottom and/or lateral boundary conditions. Its specification |
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| 149 | depends on the nature of the physical parameterisation used for ${\rm {\bf D}}^{\rm {\bf U}}$ |
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| 150 | in \eqref{Eq_PE_dyn}. It is discussed in \S\ref{PE_zdf}, page~\pageref{PE_zdf}.% and Chap. III.6 to 9. |
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| 151 | \item[Atmosphere - ocean interface:] the kinematic surface condition plus the mass flux |
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| 152 | of fresh water PE (the precipitation minus evaporation budget) leads to: |
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[707] | 153 | \begin{equation} \label{Eq_PE_w_sbc} |
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| 154 | w = \frac{\partial \eta }{\partial t} |
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| 155 | + \left. {{\rm {\bf U}}_h } \right|_{z=\eta } \cdot \nabla _h \left( \eta \right) |
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| 156 | + P-E |
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| 157 | \end{equation} |
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[1224] | 158 | The dynamic boundary condition, neglecting the surface tension (which removes capillary |
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| 159 | waves from the system) leads to the continuity of pressure across the interface $z=\eta$. |
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| 160 | The atmosphere and ocean also exchange horizontal momentum (wind stress), and heat. |
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| 161 | \item[Sea ice - ocean interface:] the ocean and sea ice exchange heat, salt, fresh water |
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| 162 | and momentum. The sea surface temperature is constrained to be at the freezing point |
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| 163 | at the interface. Sea ice salinity is very low ($\sim4-6 \,psu$) compared to those of the |
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| 164 | ocean ($\sim34 \,psu$). The cycle of freezing/melting is associated with fresh water and |
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| 165 | salt fluxes that cannot be neglected. |
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[707] | 166 | \end{description} |
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| 167 | |
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| 168 | |
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[1831] | 169 | \newpage |
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| 170 | $\ $\newline % force a new ligne |
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| 171 | |
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[707] | 172 | % ================================================================ |
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| 173 | % The Horizontal Pressure Gradient |
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| 174 | % ================================================================ |
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| 175 | \section{The Horizontal Pressure Gradient } |
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| 176 | \label{PE_hor_pg} |
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| 177 | |
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| 178 | % ------------------------------------------------------------------------------------------------------------- |
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| 179 | % Pressure Formulation |
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| 180 | % ------------------------------------------------------------------------------------------------------------- |
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| 181 | \subsection{Pressure Formulation} |
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| 182 | \label{PE_p_formulation} |
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| 183 | |
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[1224] | 184 | The total pressure at a given depth $z$ is composed of a surface pressure $p_s$ at a |
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| 185 | reference geopotential surface ($z=0$) and a hydrostatic pressure $p_h$ such that: |
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| 186 | $p(i,j,k,t)=p_s(i,j,t)+p_h(i,j,k,t)$. The latter is computed by integrating (\ref{Eq_PE_hydrostatic}), |
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| 187 | assuming that pressure in decibars can be approximated by depth in meters in (\ref{Eq_PE_eos}). |
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| 188 | The hydrostatic pressure is then given by: |
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[707] | 189 | \begin{equation} \label{Eq_PE_pressure} |
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| 190 | p_h \left( {i,j,z,t} \right) |
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[1224] | 191 | = \int_{\varsigma =z}^{\varsigma =0} {g\;\rho \left( {T,S,\varsigma} \right)\;d\varsigma } |
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[707] | 192 | \end{equation} |
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[1224] | 193 | Two strategies can be considered for the surface pressure term: $(a)$ introduce of a |
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| 194 | new variable $\eta$, the free-surface elevation, for which a prognostic equation can be |
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| 195 | established and solved; $(b)$ assume that the ocean surface is a rigid lid, on which the |
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| 196 | pressure (or its horizontal gradient) can be diagnosed. When the former strategy is used, |
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| 197 | one solution of the free-surface elevation consists of the excitation of external gravity waves. |
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| 198 | The flow is barotropic and the surface moves up and down with gravity as the restoring force. |
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| 199 | The phase speed of such waves is high (some hundreds of metres per second) so that |
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| 200 | the time step would have to be very short if they were present in the model. The latter |
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| 201 | strategy filters out these waves since the rigid lid approximation implies $\eta=0$, $i.e.$ |
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| 202 | the sea surface is the surface $z=0$. This well known approximation increases the surface |
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| 203 | wave speed to infinity and modifies certain other longwave dynamics ($e.g.$ barotropic |
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[1831] | 204 | Rossby or planetary waves). The rigid-lid hypothesis is an obsolescent feature in modern |
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| 205 | OGCMs. It has been available until the release 3.1 of \NEMO, and it has been removed |
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| 206 | in release 3.2 and followings. Only the free surface formulation is now described in the |
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| 207 | this document (see the next sub-section). |
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[707] | 208 | |
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| 209 | % ------------------------------------------------------------------------------------------------------------- |
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| 210 | % Free Surface Formulation |
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| 211 | % ------------------------------------------------------------------------------------------------------------- |
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| 212 | \subsection{Free Surface Formulation} |
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| 213 | \label{PE_free_surface} |
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| 214 | |
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[1224] | 215 | In the free surface formulation, a variable $\eta$, the sea-surface height, is introduced |
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| 216 | which describes the shape of the air-sea interface. This variable is solution of a |
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| 217 | prognostic equation which is established by forming the vertical average of the kinematic |
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| 218 | surface condition (\ref{Eq_PE_w_bbc}): |
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[707] | 219 | \begin{equation} \label{Eq_PE_ssh} |
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| 220 | \frac{\partial \eta }{\partial t}=-D+P-E |
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| 221 | \quad \text{where} \ |
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| 222 | D=\nabla \cdot \left[ {\left( {H+\eta } \right) \; {\rm{\bf \overline{U}}}_h \,} \right] |
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| 223 | \end{equation} |
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| 224 | and using (\ref{Eq_PE_hydrostatic}) the surface pressure is given by: $p_s = \rho \, g \, \eta$. |
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| 225 | |
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[1224] | 226 | Allowing the air-sea interface to move introduces the external gravity waves (EGWs) |
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| 227 | as a class of solution of the primitive equations. These waves are barotropic because |
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| 228 | of hydrostatic assumption, and their phase speed is quite high. Their time scale is |
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| 229 | short with respect to the other processes described by the primitive equations. |
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[707] | 230 | |
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[1831] | 231 | Two choices can be made regarding the implementation of the free surface in the model, |
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[1224] | 232 | depending on the physical processes of interest. |
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[707] | 233 | |
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| 234 | $\bullet$ If one is interested in EGWs, in particular the tides and their interaction |
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[1224] | 235 | with the baroclinic structure of the ocean (internal waves) possibly in shallow seas, |
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| 236 | then a non linear free surface is the most appropriate. This means that no |
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| 237 | approximation is made in (\ref{Eq_PE_ssh}) and that the variation of the ocean |
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| 238 | volume is fully taken into account. Note that in order to study the fast time scales |
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| 239 | associated with EGWs it is necessary to minimize time filtering effects (use an |
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| 240 | explicit time scheme with very small time step, or a split-explicit scheme with |
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| 241 | reasonably small time step, see \S\ref{DYN_spg_exp} or \S\ref{DYN_spg_ts}. |
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[707] | 242 | |
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| 243 | $\bullet$ If one is not interested in EGW but rather sees them as high frequency |
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[817] | 244 | noise, it is possible to apply an explicit filter to slow down the fastest waves while |
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| 245 | not altering the slow barotropic Rossby waves. If further, an approximative conservation |
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| 246 | of heat and salt contents is sufficient for the problem solved, then it is |
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| 247 | sufficient to solve a linearized version of (\ref{Eq_PE_ssh}), which still allows |
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[1831] | 248 | to take into account freshwater fluxes applied at the ocean surface \citep{Roullet_Madec_JGR00}. |
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[707] | 249 | |
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[1224] | 250 | The filtering of EGWs in models with a free surface is usually a matter of discretisation |
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[1831] | 251 | of the temporal derivatives, using the time splitting method \citep{Killworth_al_JPO91, Zhang_Endoh_JGR92} |
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[1224] | 252 | or the implicit scheme \citep{Dukowicz1994}. In \NEMO, we use a slightly different approach |
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[1831] | 253 | developed by \citet{Roullet_Madec_JGR00}: the damping of EGWs is ensured by introducing an |
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[1224] | 254 | additional force in the momentum equation. \eqref{Eq_PE_dyn} becomes: |
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[707] | 255 | \begin{equation} \label{Eq_PE_flt} |
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| 256 | \frac{\partial {\rm {\bf U}}_h }{\partial t}= {\rm {\bf M}} |
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| 257 | - g \nabla \left( \tilde{\rho} \ \eta \right) |
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| 258 | - g \ T_c \nabla \left( \widetilde{\rho} \ \partial_t \eta \right) |
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| 259 | \end{equation} |
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[1224] | 260 | where $T_c$, is a parameter with dimensions of time which characterizes the force, |
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| 261 | $\widetilde{\rho} = \rho / \rho_o$ is the dimensionless density, and $\rm {\bf M}$ |
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| 262 | represents the collected contributions of the Coriolis, hydrostatic pressure gradient, |
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| 263 | non-linear and viscous terms in \eqref{Eq_PE_dyn}. |
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[707] | 264 | |
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[1224] | 265 | The new force can be interpreted as a diffusion of vertically integrated volume flux divergence. |
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| 266 | The time evolution of $D$ is thus governed by a balance of two terms, $-g$ \textbf{A} $\eta$ |
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| 267 | and $g \, T_c \,$ \textbf{A} $D$, associated with a propagative regime and a diffusive regime |
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| 268 | in the temporal spectrum, respectively. In the diffusive regime, the EGWs no longer propagate, |
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| 269 | $i.e.$ they are stationary and damped. The diffusion regime applies to the modes shorter than |
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| 270 | $T_c$. For longer ones, the diffusion term vanishes. Hence, the temporally unresolved EGWs |
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[1831] | 271 | can be damped by choosing $T_c > \Delta t$. \citet{Roullet_Madec_JGR00} demonstrate that |
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[1224] | 272 | (\ref{Eq_PE_flt}) can be integrated with a leap frog scheme except the additional term which |
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| 273 | has to be computed implicitly. This is not surprising since the use of a large time step has a |
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| 274 | necessarily numerical cost. Two gains arise in comparison with the previous formulations. |
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| 275 | Firstly, the damping of EGWs can be quantified through the magnitude of the additional term. |
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| 276 | Secondly, the numerical scheme does not need any tuning. Numerical stability is ensured as |
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| 277 | soon as $T_c > \Delta t$. |
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[707] | 278 | |
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[1224] | 279 | When the variations of free surface elevation are small compared to the thickness of the first |
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| 280 | model layer, the free surface equation (\ref{Eq_PE_ssh}) can be linearized. As emphasized |
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[1831] | 281 | by \citet{Roullet_Madec_JGR00} the linearization of (\ref{Eq_PE_ssh}) has consequences on the |
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[1224] | 282 | conservation of salt in the model. With the nonlinear free surface equation, the time evolution |
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| 283 | of the total salt content is |
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[707] | 284 | \begin{equation} \label{Eq_PE_salt_content} |
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[1224] | 285 | \frac{\partial }{\partial t}\int\limits_{D\eta } {S\;dv} |
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| 286 | =\int\limits_S {S\;(-\frac{\partial \eta }{\partial t}-D+P-E)\;ds} |
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[707] | 287 | \end{equation} |
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[1224] | 288 | where $S$ is the salinity, and the total salt is integrated over the whole ocean volume |
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| 289 | $D_\eta$ bounded by the time-dependent free surface. The right hand side (which is an |
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| 290 | integral over the free surface) vanishes when the nonlinear equation (\ref{Eq_PE_ssh}) |
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| 291 | is satisfied, so that the salt is perfectly conserved. When the free surface equation is |
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[1831] | 292 | linearized, \citet{Roullet_Madec_JGR00} show that the total salt content integrated in the fixed |
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[1224] | 293 | volume $D$ (bounded by the surface $z=0$) is no longer conserved: |
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[707] | 294 | \begin{equation} \label{Eq_PE_salt_content_linear} |
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[1224] | 295 | \frac{\partial }{\partial t}\int\limits_D {S\;dv} |
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| 296 | = - \int\limits_S {S\;\frac{\partial \eta }{\partial t}ds} |
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[707] | 297 | \end{equation} |
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| 298 | |
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[1224] | 299 | The right hand side of (\ref{Eq_PE_salt_content_linear}) is small in equilibrium solutions |
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[1831] | 300 | \citep{Roullet_Madec_JGR00}. It can be significant when the freshwater forcing is not balanced and |
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[1224] | 301 | the globally averaged free surface is drifting. An increase in sea surface height \textit{$\eta $} |
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| 302 | results in a decrease of the salinity in the fixed volume $D$. Even in that case though, |
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| 303 | the total salt integrated in the variable volume $D_{\eta}$ varies much less, since |
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| 304 | (\ref{Eq_PE_salt_content_linear}) can be rewritten as |
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[707] | 305 | \begin{equation} \label{Eq_PE_salt_content_corrected} |
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| 306 | \frac{\partial }{\partial t}\int\limits_{D\eta } {S\;dv} |
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| 307 | =\frac{\partial}{\partial t} \left[ \;{\int\limits_D {S\;dv} +\int\limits_S {S\eta \;ds} } \right] |
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| 308 | =\int\limits_S {\eta \;\frac{\partial S}{\partial t}ds} |
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| 309 | \end{equation} |
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| 310 | |
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[1224] | 311 | Although the total salt content is not exactly conserved with the linearized free surface, |
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| 312 | its variations are driven by correlations of the time variation of surface salinity with the |
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| 313 | sea surface height, which is a negligible term. This situation contrasts with the case of |
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[1831] | 314 | the rigid lid approximation in which case freshwater forcing is represented by a virtual |
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| 315 | salt flux, leading to a spurious source of salt at the ocean surface |
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| 316 | \citep{Huang_JPO93, Roullet_Madec_JGR00}. |
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[707] | 317 | |
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| 318 | |
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| 319 | % ================================================================ |
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| 320 | % Curvilinear z-coordinate System |
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| 321 | % ================================================================ |
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| 322 | \section{Curvilinear \textit{z-}coordinate System} |
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| 323 | \label{PE_zco} |
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| 324 | |
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| 325 | |
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| 326 | % ------------------------------------------------------------------------------------------------------------- |
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| 327 | % Tensorial Formalism |
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| 328 | % ------------------------------------------------------------------------------------------------------------- |
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| 329 | \subsection{Tensorial Formalism} |
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| 330 | \label{PE_tensorial} |
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| 331 | |
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[1224] | 332 | In many ocean circulation problems, the flow field has regions of enhanced dynamics |
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| 333 | ($i.e.$ surface layers, western boundary currents, equatorial currents, or ocean fronts). |
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| 334 | The representation of such dynamical processes can be improved by specifically increasing |
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| 335 | the model resolution in these regions. As well, it may be convenient to use a lateral |
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| 336 | boundary-following coordinate system to better represent coastal dynamics. Moreover, |
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| 337 | the common geographical coordinate system has a singular point at the North Pole that |
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| 338 | cannot be easily treated in a global model without filtering. A solution consists of introducing |
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| 339 | an appropriate coordinate transformation that shifts the singular point onto land |
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[1831] | 340 | \citep{Madec_Imbard_CD96, Murray_JCP96}. As a consequence, it is important to solve the primitive |
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[1224] | 341 | equations in various curvilinear coordinate systems. An efficient way of introducing an |
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| 342 | appropriate coordinate transform can be found when using a tensorial formalism. |
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| 343 | This formalism is suited to any multidimensional curvilinear coordinate system. Ocean |
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| 344 | modellers mainly use three-dimensional orthogonal grids on the sphere (spherical earth |
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| 345 | approximation), with preservation of the local vertical. Here we give the simplified equations |
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| 346 | for this particular case. The general case is detailed by \citet{Eiseman1980} in their survey |
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| 347 | of the conservation laws of fluid dynamics. |
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[707] | 348 | |
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[1831] | 349 | Let (\textit{i},\textit{j},\textit{k}) be a set of orthogonal curvilinear coordinates on the sphere |
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[1224] | 350 | associated with the positively oriented orthogonal set of unit vectors (\textbf{i},\textbf{j},\textbf{k}) |
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| 351 | linked to the earth such that \textbf{k} is the local upward vector and (\textbf{i},\textbf{j}) are |
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| 352 | two vectors orthogonal to \textbf{k}, $i.e.$ along geopotential surfaces (Fig.\ref{Fig_referential}). |
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| 353 | Let $(\lambda,\varphi,z)$ be the geographical coordinate system in which a position is defined |
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| 354 | by the latitude $\varphi(i,j)$, the longitude $\lambda(i,j)$ and the distance from the centre of |
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| 355 | the earth $a+z(k)$ where $a$ is the earth's radius and $z$ the altitude above a reference sea |
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| 356 | level (Fig.\ref{Fig_referential}). The local deformation of the curvilinear coordinate system is |
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| 357 | given by $e_1$, $e_2$ and $e_3$, the three scale factors: |
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[707] | 358 | \begin{equation} \label{Eq_scale_factors} |
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| 359 | \begin{aligned} |
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| 360 | e_1 &=\left( {a+z} \right)\;\left[ {\left( {\frac{\partial \lambda |
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| 361 | }{\partial i}\cos \varphi } \right)^2+\left( {\frac{\partial \varphi |
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| 362 | }{\partial i}} \right)^2} \right]^{1/2} \\ |
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| 363 | e_2 &=\left( {a+z} \right)\;\left[ {\left( {\frac{\partial \lambda |
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| 364 | }{\partial j}\cos \varphi } \right)^2+\left( {\frac{\partial \varphi |
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| 365 | }{\partial j}} \right)^2} \right]^{1/2} \\ |
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| 366 | e_3 &=\left( {\frac{\partial z}{\partial k}} \right) \\ |
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| 367 | \end{aligned} |
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| 368 | \end{equation} |
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| 369 | |
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| 370 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 371 | \begin{figure}[!tb] \label{Fig_referential} \begin{center} |
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[998] | 372 | \includegraphics[width=0.60\textwidth]{./TexFiles/Figures/Fig_I_earth_referential.pdf} |
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[1224] | 373 | \caption{the geographical coordinate system $(\lambda,\varphi,z)$ and the curvilinear |
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| 374 | coordinate system (\textbf{i},\textbf{j},\textbf{k}). } |
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[707] | 375 | \end{center} \end{figure} |
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| 376 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 377 | |
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[1224] | 378 | Since the ocean depth is far smaller than the earth's radius, $a+z$, can be replaced by |
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| 379 | $a$ in (\ref{Eq_scale_factors}) (thin-shell approximation). The resulting horizontal scale |
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| 380 | factors $e_1$, $e_2$ are independent of $k$ while the vertical scale factor is a single |
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| 381 | function of $k$ as \textbf{k} is parallel to \textbf{z}. The scalar and vector operators that |
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| 382 | appear in the primitive equations (Eqs. \eqref{Eq_PE_dyn} to \eqref{Eq_PE_eos}) can |
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| 383 | be written in the tensorial form, invariant in any orthogonal horizontal curvilinear coordinate |
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| 384 | system transformation: |
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[707] | 385 | \begin{subequations} \label{Eq_PE_discrete_operators} |
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| 386 | \begin{equation} \label{Eq_PE_grad} |
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| 387 | \nabla q=\frac{1}{e_1 }\frac{\partial q}{\partial i}\;{\rm {\bf |
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| 388 | i}}+\frac{1}{e_2 }\frac{\partial q}{\partial j}\;{\rm {\bf j}}+\frac{1}{e_3 |
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| 389 | }\frac{\partial q}{\partial k}\;{\rm {\bf k}} \\ |
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| 390 | \end{equation} |
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| 391 | \begin{equation} \label{Eq_PE_div} |
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| 392 | \nabla \cdot {\rm {\bf A}} |
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| 393 | = \frac{1}{e_1 \; e_2} \left[ |
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| 394 | \frac{\partial \left(e_2 \; a_1\right)}{\partial i } |
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| 395 | +\frac{\partial \left(e_1 \; a_2\right)}{\partial j } \right] |
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| 396 | + \frac{1}{e_3} \left[ \frac{\partial a_3}{\partial k } \right] |
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| 397 | \end{equation} |
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| 398 | \begin{equation} \label{Eq_PE_curl} |
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| 399 | \begin{split} |
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| 400 | \nabla \times \vect{A} = |
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| 401 | \left[ {\frac{1}{e_2 }\frac{\partial a_3}{\partial j} |
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| 402 | -\frac{1}{e_3 }\frac{\partial a_2 }{\partial k}} \right] \; \vect{i} |
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| 403 | &+\left[ {\frac{1}{e_3 }\frac{\partial a_1 }{\partial k} |
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| 404 | -\frac{1}{e_1 }\frac{\partial a_3 }{\partial i}} \right] \; \vect{j} \\ |
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| 405 | &+\frac{1}{e_1 e_2 } \left[ {\frac{\partial \left( {e_2 a_2 } \right)}{\partial i} |
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| 406 | -\frac{\partial \left( {e_1 a_1 } \right)}{\partial j}} \right] \; \vect{k} |
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| 407 | \end{split} |
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| 408 | \end{equation} |
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| 409 | \begin{equation} \label{Eq_PE_lap} |
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| 410 | \Delta q = \nabla \cdot \left( \nabla q \right) |
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| 411 | \end{equation} |
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| 412 | \begin{equation} \label{Eq_PE_lap_vector} |
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| 413 | \Delta {\rm {\bf A}} = |
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| 414 | \nabla \left( \nabla \cdot {\rm {\bf A}} \right) |
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| 415 | - \nabla \times \left( \nabla \times {\rm {\bf A}} \right) |
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| 416 | \end{equation} |
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| 417 | \end{subequations} |
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[817] | 418 | where $q$ is a scalar quantity and ${\rm {\bf A}}=(a_1,a_2,a_3)$ a vector in the $(i,j,k)$ coordinate system. |
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[707] | 419 | |
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| 420 | % ------------------------------------------------------------------------------------------------------------- |
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| 421 | % Continuous Model Equations |
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| 422 | % ------------------------------------------------------------------------------------------------------------- |
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| 423 | \subsection{Continuous Model Equations} |
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| 424 | \label{PE_zco_Eq} |
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| 425 | |
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[1224] | 426 | In order to express the Primitive Equations in tensorial formalism, it is necessary to compute |
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| 427 | the horizontal component of the non-linear and viscous terms of the equation using |
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| 428 | \eqref{Eq_PE_grad}) to \eqref{Eq_PE_lap_vector}. |
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| 429 | Let us set $\vect U=(u,v,w)={\vect{U}}_h +w\;\vect{k}$, the velocity in the $(i,j,k)$ coordinate |
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| 430 | system and define the relative vorticity $\zeta$ and the divergence of the horizontal velocity |
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| 431 | field $\chi$, by: |
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[707] | 432 | \begin{equation} \label{Eq_PE_curl_Uh} |
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| 433 | \zeta =\frac{1}{e_1 e_2 }\left[ {\frac{\partial \left( {e_2 \,v} |
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| 434 | \right)}{\partial i}-\frac{\partial \left( {e_1 \,u} \right)}{\partial j}} |
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| 435 | \right] |
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| 436 | \end{equation} |
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| 437 | \begin{equation} \label{Eq_PE_div_Uh} |
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| 438 | \chi =\frac{1}{e_1 e_2 }\left[ {\frac{\partial \left( {e_2 \,u} |
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| 439 | \right)}{\partial i}+\frac{\partial \left( {e_1 \,v} \right)}{\partial j}} |
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| 440 | \right] |
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| 441 | \end{equation} |
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| 442 | |
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[1224] | 443 | Using the fact that the horizontal scale factors $e_1$ and $e_2$ are independent of $k$ |
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| 444 | and that $e_3$ is a function of the single variable $k$, the nonlinear term of |
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| 445 | \eqref{Eq_PE_dyn} can be transformed as follows: |
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[707] | 446 | \begin{flalign*} |
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| 447 | &\left[ {\left( { \nabla \times {\rm {\bf U}} } \right) \times {\rm {\bf U}} |
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| 448 | +\frac{1}{2} \nabla \left( {{\rm {\bf U}}^2} \right)} \right]_h & |
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| 449 | \end{flalign*} |
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| 450 | \begin{flalign*} |
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[817] | 451 | &\qquad=\left( {{\begin{array}{*{20}c} |
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[707] | 452 | {\left[ { \frac{1}{e_3} \frac{\partial u }{\partial k} |
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| 453 | -\frac{1}{e_1} \frac{\partial w }{\partial i} } \right] w - \zeta \; v } \\ |
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| 454 | {\zeta \; u - \left[ { \frac{1}{e_2} \frac{\partial w}{\partial j} |
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| 455 | -\frac{1}{e_3} \frac{\partial v}{\partial k} } \right] \ w} \\ |
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| 456 | \end{array} }} \right) |
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| 457 | +\frac{1}{2} \left( {{\begin{array}{*{20}c} |
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| 458 | { \frac{1}{e_1} \frac{\partial \left( u^2+v^2+w^2 \right)}{\partial i}} \hfill \\ |
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| 459 | { \frac{1}{e_2} \frac{\partial \left( u^2+v^2+w^2 \right)}{\partial j}} \hfill \\ |
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| 460 | \end{array} }} \right) & |
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| 461 | \end{flalign*} |
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| 462 | \begin{flalign*} |
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[817] | 463 | & \qquad =\left( {{ \begin{array}{*{20}c} |
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[707] | 464 | {-\zeta \; v} \hfill \\ |
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| 465 | { \zeta \; u} \hfill \\ |
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| 466 | \end{array} }} \right) |
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| 467 | +\frac{1}{2}\left( {{ \begin{array}{*{20}c} |
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| 468 | {\frac{1}{e_1 }\frac{\partial \left( {u^2+v^2} \right)}{\partial i}} \hfill \\ |
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| 469 | {\frac{1}{e_2 }\frac{\partial \left( {u^2+v^2} \right)}{\partial j}} \hfill \\ |
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| 470 | \end{array} }} \right) |
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| 471 | +\frac{1}{e_3 }\left( {{ \begin{array}{*{20}c} |
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| 472 | { w \; \frac{\partial u}{\partial k}} \\ |
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| 473 | { w \; \frac{\partial v}{\partial k}} \\ |
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| 474 | \end{array} }} \right) |
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| 475 | -\left( {{ \begin{array}{*{20}c} |
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| 476 | {\frac{w}{e_1}\frac{\partial w}{\partial i} |
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| 477 | -\frac{1}{2e_1}\frac{\partial w^2}{\partial i}} \hfill \\ |
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| 478 | {\frac{w}{e_2}\frac{\partial w}{\partial j} |
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| 479 | -\frac{1}{2e_2}\frac{\partial w^2}{\partial j}} \hfill \\ |
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| 480 | \end{array} }} \right) & |
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| 481 | \end{flalign*} |
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| 482 | |
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[1224] | 483 | The last term of the right hand side is obviously zero, and thus the nonlinear term of |
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| 484 | \eqref{Eq_PE_dyn} is written in the $(i,j,k)$ coordinate system: |
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[707] | 485 | \begin{equation} \label{Eq_PE_vector_form} |
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| 486 | \left[ {\left( { \nabla \times {\rm {\bf U}} } \right) \times {\rm {\bf U}} |
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| 487 | +\frac{1}{2} \nabla \left( {{\rm {\bf U}}^2} \right)} \right]_h |
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| 488 | =\zeta |
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| 489 | \;{\rm {\bf k}}\times {\rm {\bf U}}_h +\frac{1}{2}\nabla _h \left( {{\rm |
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| 490 | {\bf U}}_h^2 } \right)+\frac{1}{e_3 }w\frac{\partial {\rm {\bf U}}_h |
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| 491 | }{\partial k} |
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| 492 | \end{equation} |
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| 493 | |
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[1224] | 494 | This is the so-called \textit{vector invariant form} of the momentum advection term. |
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| 495 | For some purposes, it can be advantageous to write this term in the so-called flux form, |
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| 496 | $i.e.$ to write it as the divergence of fluxes. For example, the first component of |
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| 497 | \eqref{Eq_PE_vector_form} (the $i$-component) is transformed as follows: |
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[707] | 498 | \begin{flalign*} |
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| 499 | &{ \begin{array}{*{20}l} |
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| 500 | \left[ {\left( {\nabla \times \vect{U}} \right)\times \vect{U} |
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[817] | 501 | +\frac{1}{2}\nabla \left( {\vect{U}}^2 \right)} \right]_i % \\ |
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| 502 | %\\ |
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[707] | 503 | = - \zeta \;v |
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| 504 | + \frac{1}{2\;e_1 } \frac{\partial \left( {u^2+v^2} \right)}{\partial i} |
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| 505 | + \frac{1}{e_3}w \ \frac{\partial u}{\partial k} \\ |
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| 506 | \\ |
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[817] | 507 | \qquad =\frac{1}{e_1 \; e_2} \left( -v\frac{\partial \left( {e_2 \,v} \right)}{\partial i} |
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[707] | 508 | +v\frac{\partial \left( {e_1 \,u} \right)}{\partial j} \right) |
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| 509 | +\frac{1}{e_1 e_2 }\left( +e_2 \; u\frac{\partial u}{\partial i} |
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| 510 | +e_2 \; v\frac{\partial v}{\partial i} \right) |
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| 511 | +\frac{1}{e_3} \left( w\;\frac{\partial u}{\partial k} \right) \\ |
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| 512 | \end{array} } & |
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| 513 | \end{flalign*} |
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| 514 | \begin{flalign*} |
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| 515 | &{ \begin{array}{*{20}l} |
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[817] | 516 | \qquad =\frac{1}{e_1 \; e_2} \left\{ |
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[707] | 517 | -\left( v^2 \frac{\partial e_2 }{\partial i} |
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| 518 | +e_2 \,v \frac{\partial v }{\partial i} \right) |
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| 519 | +\left( \frac{\partial \left( {e_1 \,u\,v} \right)}{\partial j} |
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| 520 | -e_1 \,u \frac{\partial v }{\partial j} \right) \right. |
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| 521 | \\ \left. \qquad \qquad \quad |
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| 522 | +\left( \frac{\partial \left( {e_2 u\,u} \right)}{\partial i} |
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| 523 | -u \frac{\partial \left( {e_2 u} \right)}{\partial i} \right) |
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| 524 | +e_2 v \frac{\partial v }{\partial i} |
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| 525 | \right\} |
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| 526 | +\frac{1}{e_3} \left( |
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[817] | 527 | \frac{\partial \left( {w\,u} \right) }{\partial k} |
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[707] | 528 | -u \frac{\partial w }{\partial k} \right) \\ |
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| 529 | \end{array} } & |
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| 530 | \end{flalign*} |
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| 531 | \begin{flalign*} |
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| 532 | &{ \begin{array}{*{20}l} |
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[817] | 533 | \qquad =\frac{1}{e_1 \; e_2} \left( |
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[707] | 534 | \frac{\partial \left( {e_2 \,u\,u} \right)}{\partial i} |
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| 535 | + \frac{\partial \left( {e_1 \,u\,v} \right)}{\partial j} \right) |
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[817] | 536 | +\frac{1}{e_3 } \frac{\partial \left( {w\,u } \right)}{\partial k} |
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[707] | 537 | \\ \qquad \qquad \quad |
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| 538 | +\frac{1}{e_1 e_2 } \left( |
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| 539 | -u \left( \frac{\partial \left( {e_1 v } \right)}{\partial j} |
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| 540 | -v\,\frac{\partial e_1 }{\partial j} \right) |
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| 541 | -u \frac{\partial \left( {e_2 u } \right)}{\partial i} |
---|
| 542 | \right) |
---|
| 543 | -\frac{1}{e_3 } \frac{\partial w}{\partial k} u |
---|
| 544 | +\frac{1}{e_1 e_2 }\left( -v^2\frac{\partial e_2 }{\partial i} \right) |
---|
| 545 | \end{array} } & |
---|
| 546 | \end{flalign*} |
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| 547 | \begin{flalign*} |
---|
| 548 | &{ \begin{array}{*{20}l} |
---|
[817] | 549 | \qquad = \nabla \cdot \left( {{\rm {\bf U}}\,u} \right) |
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| 550 | - \left( \nabla \cdot {\rm {\bf U}} \right) \ u |
---|
[707] | 551 | +\frac{1}{e_1 e_2 }\left( |
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| 552 | -v^2 \frac{\partial e_2 }{\partial i} |
---|
| 553 | +uv \, \frac{\partial e_1 }{\partial j} \right) \\ |
---|
| 554 | \end{array} } & |
---|
| 555 | \end{flalign*} |
---|
| 556 | as $\nabla \cdot {\rm {\bf U}}\;=0$ (incompressibility) it comes: |
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| 557 | \begin{flalign*} |
---|
| 558 | &{ \begin{array}{*{20}l} |
---|
[817] | 559 | \qquad = \nabla \cdot \left( {{\rm {\bf U}}\,u} \right) |
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[707] | 560 | + \frac{1}{e_1 e_2 } \left( v \; \frac{\partial e_2}{\partial i} |
---|
| 561 | -u \; \frac{\partial e_1}{\partial j} \right) \left( -v \right) |
---|
| 562 | \end{array} } & |
---|
| 563 | \end{flalign*} |
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| 564 | |
---|
[817] | 565 | The flux form of the momentum advection term is therefore given by: |
---|
[707] | 566 | \begin{multline} \label{Eq_PE_flux_form} |
---|
| 567 | \left[ |
---|
| 568 | \left( {\nabla \times {\rm {\bf U}}} \right) \times {\rm {\bf U}} |
---|
| 569 | +\frac{1}{2} \nabla \left( {{\rm {\bf U}}^2} \right) |
---|
| 570 | \right]_h |
---|
[817] | 571 | \\ |
---|
| 572 | = \nabla \cdot \left( {{\begin{array}{*{20}c} {\rm {\bf U}} \, u \hfill \\ |
---|
[707] | 573 | {\rm {\bf U}} \, v \hfill \\ |
---|
| 574 | \end{array} }} |
---|
| 575 | \right) |
---|
| 576 | +\frac{1}{e_1 e_2 } \left( |
---|
| 577 | v\frac{\partial e_2}{\partial i} |
---|
| 578 | -u\frac{\partial e_1}{\partial j} |
---|
| 579 | \right) {\rm {\bf k}} \times {\rm {\bf U}}_h |
---|
| 580 | \end{multline} |
---|
| 581 | |
---|
[1224] | 582 | The flux form has two terms, the first one is expressed as the divergence of momentum |
---|
| 583 | fluxes (hence the flux form name given to this formulation) and the second one is due to |
---|
| 584 | the curvilinear nature of the coordinate system used. The latter is called the \emph{metric} |
---|
| 585 | term and can be viewed as a modification of the Coriolis parameter: |
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[707] | 586 | \begin{equation} \label{Eq_PE_cor+metric} |
---|
[1831] | 587 | f \to f + \frac{1}{e_1\;e_2} \left( v \frac{\partial e_2}{\partial i} |
---|
| 588 | -u \frac{\partial e_1}{\partial j} \right) |
---|
[707] | 589 | \end{equation} |
---|
| 590 | |
---|
[1224] | 591 | Note that in the case of geographical coordinate, $i.e.$ when $(i,j) \to (\lambda ,\varphi )$ |
---|
| 592 | and $(e_1 ,e_2) \to (a \,\cos \varphi ,a)$, we recover the commonly used modification of |
---|
| 593 | the Coriolis parameter $f \to f+(u/a) \tan \varphi$. |
---|
[707] | 594 | |
---|
[1831] | 595 | |
---|
| 596 | $\ $\newline % force a new ligne |
---|
| 597 | |
---|
[817] | 598 | To sum up, the equations solved by the ocean model can be written in the following tensorial formalism: |
---|
[707] | 599 | |
---|
[817] | 600 | \vspace{+10pt} |
---|
[1831] | 601 | $\bullet$ \textbf{Vector invariant form of the momentum equations} : |
---|
[817] | 602 | |
---|
[707] | 603 | \begin{subequations} \label{Eq_PE_dyn_vect} |
---|
[1831] | 604 | \begin{equation} \label{Eq_PE_dyn_vect_u} \begin{split} |
---|
| 605 | \frac{\partial u}{\partial t} |
---|
| 606 | = + \left( {\zeta +f} \right)\,v |
---|
| 607 | - \frac{1}{2\,e_1} \frac{\partial}{\partial i} \left( u^2+v^2 \right) |
---|
| 608 | - \frac{1}{e_3 } w \frac{\partial u}{\partial k} & \\ |
---|
| 609 | - \frac{1}{e_1 } \frac{\partial}{\partial i} \left( \frac{p_s+p_h }{\rho _o} \right) |
---|
| 610 | &+ D_u^{\vect{U}} + F_u^{\vect{U}} \\ |
---|
| 611 | \\ |
---|
| 612 | \frac{\partial v}{\partial t} = |
---|
| 613 | - \left( {\zeta +f} \right)\,u |
---|
| 614 | - \frac{1}{2\,e_2 } \frac{\partial }{\partial j}\left( u^2+v^2 \right) |
---|
| 615 | - \frac{1}{e_3 } w \frac{\partial v}{\partial k} & \\ |
---|
| 616 | - \frac{1}{e_2 } \frac{\partial }{\partial j}\left( \frac{p_s+p_h }{\rho _o} \right) |
---|
| 617 | &+ D_v^{\vect{U}} + F_v^{\vect{U}} |
---|
| 618 | \end{split} \end{equation} |
---|
[707] | 619 | \end{subequations} |
---|
| 620 | |
---|
[1831] | 621 | |
---|
| 622 | \vspace{+10pt} |
---|
| 623 | $\bullet$ \textbf{flux form of the momentum equations} : |
---|
[817] | 624 | \begin{subequations} \label{Eq_PE_dyn_flux} |
---|
| 625 | \begin{multline} \label{Eq_PE_dyn_flux_u} |
---|
| 626 | \frac{\partial u}{\partial t}= |
---|
| 627 | + \left( { f + \frac{1}{e_1 \; e_2} |
---|
| 628 | \left( v \frac{\partial e_2}{\partial i} |
---|
| 629 | -u \frac{\partial e_1}{\partial j} \right)} \right) \, v \\ |
---|
| 630 | - \frac{1}{e_1 \; e_2} \left( |
---|
| 631 | \frac{\partial \left( {e_2 \,u\,u} \right)}{\partial i} |
---|
| 632 | + \frac{\partial \left( {e_1 \,v\,u} \right)}{\partial j} \right) |
---|
[994] | 633 | - \frac{1}{e_3 }\frac{\partial \left( { w\,u} \right)}{\partial k} \\ |
---|
[817] | 634 | - \frac{1}{e_1 }\frac{\partial}{\partial i}\left( \frac{p_s+p_h }{\rho _o} \right) |
---|
| 635 | + D_u^{\vect{U}} + F_u^{\vect{U}} |
---|
| 636 | \end{multline} |
---|
| 637 | \begin{multline} \label{Eq_PE_dyn_flux_v} |
---|
| 638 | \frac{\partial v}{\partial t}= |
---|
| 639 | - \left( { f + \frac{1}{e_1 \; e_2} |
---|
| 640 | \left( v \frac{\partial e_2}{\partial i} |
---|
| 641 | -u \frac{\partial e_1}{\partial j} \right)} \right) \, u \\ |
---|
| 642 | \frac{1}{e_1 \; e_2} \left( |
---|
| 643 | \frac{\partial \left( {e_2 \,u\,v} \right)}{\partial i} |
---|
[994] | 644 | + \frac{\partial \left( {e_1 \,v\,v} \right)}{\partial j} \right) |
---|
| 645 | - \frac{1}{e_3 } \frac{\partial \left( { w\,v} \right)}{\partial k} \\ |
---|
[817] | 646 | - \frac{1}{e_2 }\frac{\partial }{\partial j}\left( \frac{p_s+p_h }{\rho _o} \right) |
---|
| 647 | + D_v^{\vect{U}} + F_v^{\vect{U}} |
---|
| 648 | \end{multline} |
---|
| 649 | \end{subequations} |
---|
[1831] | 650 | where $\zeta$, the relative vorticity, is given by \eqref{Eq_PE_curl_Uh} and $p_s $, |
---|
| 651 | the surface pressure, is given by: |
---|
| 652 | \begin{equation} \label{Eq_PE_spg} |
---|
| 653 | p_s = \left\{ \begin{split} |
---|
| 654 | \rho \,g \,\eta & \qquad \qquad \; \qquad \text{ standard free surface} \\ |
---|
| 655 | \rho \,g \,\eta &+ \rho_o \,\mu \,\frac{\partial \eta }{\partial t} \qquad \text{ filtered free surface} |
---|
| 656 | \end{split} |
---|
| 657 | \right. |
---|
[707] | 658 | \end{equation} |
---|
[1831] | 659 | with $\eta$ is solution of \eqref{Eq_PE_ssh} |
---|
[707] | 660 | |
---|
| 661 | The vertical velocity and the hydrostatic pressure are diagnosed from the following equations: |
---|
| 662 | \begin{equation} \label{Eq_w_diag} |
---|
| 663 | \frac{\partial w}{\partial k}=-\chi \;e_3 |
---|
| 664 | \end{equation} |
---|
| 665 | \begin{equation} \label{Eq_hp_diag} |
---|
| 666 | \frac{\partial p_h }{\partial k}=-\rho \;g\;e_3 |
---|
| 667 | \end{equation} |
---|
[817] | 668 | where the divergence of the horizontal velocity, $\chi$ is given by \eqref{Eq_PE_div_Uh}. |
---|
[707] | 669 | |
---|
[817] | 670 | \vspace{+10pt} |
---|
| 671 | $\bullet$ \textit{tracer equations} : |
---|
[707] | 672 | \begin{equation} \label{Eq_S} |
---|
[817] | 673 | \frac{\partial T}{\partial t} = |
---|
| 674 | -\frac{1}{e_1 e_2 }\left[ { \frac{\partial \left( {e_2 T\,u} \right)}{\partial i} |
---|
| 675 | +\frac{\partial \left( {e_1 T\,v} \right)}{\partial j}} \right] |
---|
| 676 | -\frac{1}{e_3 }\frac{\partial \left( {T\,w} \right)}{\partial k} + D^T + F^T |
---|
[707] | 677 | \end{equation} |
---|
| 678 | \begin{equation} \label{Eq_T} |
---|
[817] | 679 | \frac{\partial S}{\partial t} = |
---|
| 680 | -\frac{1}{e_1 e_2 }\left[ {\frac{\partial \left( {e_2 S\,u} \right)}{\partial i} |
---|
| 681 | +\frac{\partial \left( {e_1 S\,v} \right)}{\partial j}} \right] |
---|
| 682 | -\frac{1}{e_3 }\frac{\partial \left( {S\,w} \right)}{\partial k} + D^S + F^S |
---|
[707] | 683 | \end{equation} |
---|
| 684 | \begin{equation} \label{Eq_rho} |
---|
| 685 | \rho =\rho \left( {T,S,z(k)} \right) |
---|
| 686 | \end{equation} |
---|
| 687 | |
---|
[1224] | 688 | The expression of \textbf{D}$^{U}$, $D^{S}$ and $D^{T}$ depends on the subgrid scale |
---|
| 689 | parameterisation used. It will be defined in \S\ref{PE_zdf}. The nature and formulation of |
---|
| 690 | ${\rm {\bf F}}^{\rm {\bf U}}$, $F^T$ and $F^S$, the surface forcing terms, are discussed |
---|
| 691 | in Chapter~\ref{SBC}. |
---|
[707] | 692 | |
---|
[1831] | 693 | |
---|
[707] | 694 | \newpage |
---|
| 695 | % ================================================================ |
---|
[1831] | 696 | % Curvilinear s-coordinate System |
---|
[817] | 697 | % ================================================================ |
---|
[1831] | 698 | \section{Curvilinear \textit{s}-coordinate System} |
---|
| 699 | \label{PE_sco} |
---|
[817] | 700 | |
---|
[1831] | 701 | |
---|
| 702 | |
---|
| 703 | |
---|
| 704 | |
---|
| 705 | % ------------------------------------------------------------------------------------------------------------- |
---|
| 706 | % Curvilinear z*-coordinate System |
---|
| 707 | % ------------------------------------------------------------------------------------------------------------- |
---|
| 708 | \subsection{Curvilinear \textit{z*}-coordinate System} |
---|
| 709 | \label{PE_zco_star} |
---|
| 710 | |
---|
[817] | 711 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
| 712 | \begin{figure}[!b] \label{Fig_z_zstar} \begin{center} |
---|
[998] | 713 | \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_z_zstar.pdf} |
---|
[1224] | 714 | \caption{(a) $z$-coordinate in linear free-surface case ; (b) $z-$coordinate in non-linear |
---|
| 715 | free surface case (c) re-scaled height coordinate (become popular as the \textit{z*-}coordinate |
---|
| 716 | \citep{Adcroft_Campin_OM04} ).} |
---|
[817] | 717 | \end{center} \end{figure} |
---|
| 718 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
| 719 | |
---|
| 720 | |
---|
[1224] | 721 | In that case, the free surface equation is nonlinear, and the variations of volume are fully |
---|
| 722 | taken into account. These coordinates systems is presented in a report \citep{Levier2007} |
---|
| 723 | available on the \NEMO web site. |
---|
[817] | 724 | |
---|
| 725 | \gmcomment{ |
---|
[1224] | 726 | The \textit{z*} coordinate approach is an unapproximated, non-linear free surface implementation |
---|
| 727 | which allows one to deal with large amplitude free-surface |
---|
[817] | 728 | variations relative to the vertical resolution \citep{Adcroft_Campin_OM04}. In |
---|
| 729 | the \textit{z*} formulation, the variation of the column thickness due to sea-surface |
---|
| 730 | undulations is not concentrated in the surface level, as in the $z$-coordinate formulation, |
---|
| 731 | but is equally distributed over the full water column. Thus vertical |
---|
| 732 | levels naturally follow sea-surface variations, with a linear attenuation with |
---|
| 733 | depth, as illustrated by figure fig.1c . Note that with a flat bottom, such as in |
---|
| 734 | fig.1c, the bottom-following $z$ coordinate and \textit{z*} are equivalent. |
---|
| 735 | The definition and modified oceanic equations for the rescaled vertical coordinate |
---|
| 736 | \textit{z*}, including the treatment of fresh-water flux at the surface, are |
---|
| 737 | detailed in Adcroft and Campin (2004). The major points are summarized |
---|
| 738 | here. The position ( \textit{z*}) and vertical discretization (\textit{z*}) are expressed as: |
---|
| 739 | |
---|
| 740 | $H + \textit{z*} = (H + z) / r$ and $\delta \textit{z*} = \delta z / r$ with $r = \frac{H+\eta} {H}$ |
---|
| 741 | |
---|
| 742 | Since the vertical displacement of the free surface is incorporated in the vertical |
---|
[1224] | 743 | coordinate \textit{z*}, the upper and lower boundaries are at fixed \textit{z*} position, |
---|
| 744 | $\textit{z*} = 0$ and $\textit{z*} = ?H$ respectively. Also the divergence of the flow field |
---|
| 745 | is no longer zero as shown by the continuity equation: |
---|
[817] | 746 | |
---|
| 747 | $\frac{\partial r}{\partial t} = \nabla_{\textit{z*}} \cdot \left( r \; \rm{\bf U}_h \right) |
---|
| 748 | \left( r \; w\textit{*} \right) = 0 $ |
---|
| 749 | |
---|
| 750 | } |
---|
| 751 | |
---|
| 752 | |
---|
| 753 | \newpage |
---|
[1831] | 754 | % ------------------------------------------------------------------------------------------------------------- |
---|
| 755 | % Terrain following coordinate System |
---|
| 756 | % ------------------------------------------------------------------------------------------------------------- |
---|
| 757 | \subsection{Terrain following \textit{s-}coordinate} |
---|
[707] | 758 | \label{PE_sco} |
---|
| 759 | |
---|
| 760 | % ------------------------------------------------------------------------------------------------------------- |
---|
| 761 | % Introduction |
---|
| 762 | % ------------------------------------------------------------------------------------------------------------- |
---|
[1831] | 763 | \subsubsection{Introduction} |
---|
[707] | 764 | |
---|
[1224] | 765 | Several important aspects of the ocean circulation are influenced by bottom topography. |
---|
| 766 | Of course, the most important is that bottom topography determines deep ocean sub-basins, |
---|
| 767 | barriers, sills and channels that strongly constrain the path of water masses, but more subtle |
---|
| 768 | effects exist. For example, the topographic $\beta$-effect is usually larger than the planetary |
---|
| 769 | one along continental slopes. Topographic Rossby waves can be excited and can interact |
---|
| 770 | with the mean current. In the $z-$coordinate system presented in the previous section |
---|
| 771 | (\S\ref{PE_zco}), $z-$surfaces are geopotential surfaces. The bottom topography is |
---|
| 772 | discretised by steps. This often leads to a misrepresentation of a gradually sloping bottom |
---|
| 773 | and to large localized depth gradients associated with large localized vertical velocities. |
---|
| 774 | The response to such a velocity field often leads to numerical dispersion effects. |
---|
| 775 | One solution to strongly reduce this error is to use a partial step representation of bottom |
---|
| 776 | topography instead of a full step one \cite{Pacanowski_Gnanadesikan_MWR98}. |
---|
| 777 | Another solution is to introduce a terrain-following coordinate system (hereafter $s-$coordinate) |
---|
[707] | 778 | |
---|
[1224] | 779 | The $s$-coordinate avoids the discretisation error in the depth field since the layers of |
---|
| 780 | computation are gradually adjusted with depth to the ocean bottom. Relatively small |
---|
| 781 | topographic features as well as gentle, large-scale slopes of the sea floor in the deep |
---|
| 782 | ocean, which would be ignored in typical $z$-model applications with the largest grid |
---|
| 783 | spacing at greatest depths, can easily be represented (with relatively low vertical resolution). |
---|
| 784 | A terrain-following model (hereafter $s-$model) also facilitates the modelling of the |
---|
| 785 | boundary layer flows over a large depth range, which in the framework of the $z$-model |
---|
| 786 | would require high vertical resolution over the whole depth range. Moreover, with a |
---|
| 787 | $s$-coordinate it is possible, at least in principle, to have the bottom and the sea surface |
---|
| 788 | as the only boundaries of the domain (nomore lateral boundary condition to specify). |
---|
| 789 | Nevertheless, a $s$-coordinate also has its drawbacks. Perfectly adapted to a |
---|
| 790 | homogeneous ocean, it has strong limitations as soon as stratification is introduced. |
---|
| 791 | The main two problems come from the truncation error in the horizontal pressure |
---|
| 792 | gradient and a possibly increased diapycnal diffusion. The horizontal pressure force |
---|
| 793 | in $s$-coordinate consists of two terms (see Appendix~\ref{Apdx_A}), |
---|
[707] | 794 | |
---|
| 795 | \begin{equation} \label{Eq_PE_p_sco} |
---|
| 796 | \left. {\nabla p} \right|_z =\left. {\nabla p} \right|_s -\frac{\partial |
---|
| 797 | p}{\partial s}\left. {\nabla z} \right|_s |
---|
| 798 | \end{equation} |
---|
| 799 | |
---|
[1224] | 800 | The second term in \eqref{Eq_PE_p_sco} depends on the tilt of the coordinate surface |
---|
| 801 | and introduces a truncation error that is not present in a $z$-model. In the special case |
---|
| 802 | of a $\sigma-$coordinate (i.e. a depth-normalised coordinate system $\sigma = z/H$), |
---|
| 803 | \citet{Haney1991} and \citet{Beckmann1993} have given estimates of the magnitude |
---|
| 804 | of this truncation error. It depends on topographic slope, stratification, horizontal and |
---|
| 805 | vertical resolution, the equation of state, and the finite difference scheme. This error |
---|
| 806 | limits the possible topographic slopes that a model can handle at a given horizontal |
---|
| 807 | and vertical resolution. This is a severe restriction for large-scale applications using |
---|
| 808 | realistic bottom topography. The large-scale slopes require high horizontal resolution, |
---|
| 809 | and the computational cost becomes prohibitive. This problem can be at least partially |
---|
[1831] | 810 | overcome by mixing $s$-coordinate and step-like representation of bottom topography \citep{Gerdes1993a,Gerdes1993b,Madec_al_JPO96}. However, the definition of the model |
---|
[1224] | 811 | domain vertical coordinate becomes then a non-trivial thing for a realistic bottom |
---|
| 812 | topography: a envelope topography is defined in $s$-coordinate on which a full or |
---|
| 813 | partial step bottom topography is then applied in order to adjust the model depth to |
---|
| 814 | the observed one (see \S\ref{DOM_zgr}. |
---|
[707] | 815 | |
---|
[1224] | 816 | For numerical reasons a minimum of diffusion is required along the coordinate surfaces |
---|
| 817 | of any finite difference model. It causes spurious diapycnal mixing when coordinate |
---|
| 818 | surfaces do not coincide with isoneutral surfaces. This is the case for a $z$-model as |
---|
| 819 | well as for a $s$-model. However, density varies more strongly on $s-$surfaces than |
---|
| 820 | on horizontal surfaces in regions of large topographic slopes, implying larger diapycnal |
---|
| 821 | diffusion in a $s$-model than in a $z$-model. Whereas such a diapycnal diffusion in a |
---|
| 822 | $z$-model tends to weaken horizontal density (pressure) gradients and thus the horizontal |
---|
| 823 | circulation, it usually reinforces these gradients in a $s$-model, creating spurious circulation. |
---|
| 824 | For example, imagine an isolated bump of topography in an ocean at rest with a horizontally |
---|
| 825 | uniform stratification. Spurious diffusion along $s$-surfaces will induce a bump of isoneutral |
---|
| 826 | surfaces over the topography, and thus will generate there a baroclinic eddy. In contrast, |
---|
| 827 | the ocean will stay at rest in a $z$-model. As for the truncation error, the problem can be reduced by introducing the terrain-following coordinate below the strongly stratified portion of the water column |
---|
[1831] | 828 | ($i.e.$ the main thermocline) \citep{Madec_al_JPO96}. An alternate solution consists of rotating |
---|
[1224] | 829 | the lateral diffusive tensor to geopotential or to isoneutral surfaces (see \S\ref{PE_ldf}. |
---|
| 830 | Unfortunately, the slope of isoneutral surfaces relative to the $s$-surfaces can very large, |
---|
| 831 | strongly exceeding the stability limit of such a operator when it is discretized (see Chapter~\ref{LDF}). |
---|
[707] | 832 | |
---|
[1831] | 833 | The $s-$coordinates introduced here \citep{Lott_al_OM90,Madec_al_JPO96} differ mainly in two |
---|
[1224] | 834 | aspects from similar models: it allows a representation of bottom topography with mixed |
---|
| 835 | full or partial step-like/terrain following topography ; It also offers a completely general |
---|
| 836 | transformation, $s=s(i,j,z)$ for the vertical coordinate. |
---|
[707] | 837 | |
---|
| 838 | % ------------------------------------------------------------------------------------------------------------- |
---|
| 839 | % The s-coordinate Formulation |
---|
| 840 | % ------------------------------------------------------------------------------------------------------------- |
---|
[1831] | 841 | \subsubsection{The \textit{s-}coordinate Formulation} |
---|
[707] | 842 | |
---|
[1224] | 843 | Starting from the set of equations established in \S\ref{PE_zco} for the special case $k=z$ |
---|
| 844 | and thus $e_3=1$, we introduce an arbitrary vertical coordinate $s=s(i,j,k,t)$, which includes |
---|
| 845 | $z$-, \textit{z*}- and $\sigma-$coordinates as special cases ($s=z$, $s=\textit{z*}$, and |
---|
| 846 | $s=\sigma=z/H$ or $=z/\left(H+\eta \right)$, resp.). A formal derivation of the transformed |
---|
| 847 | equations is given in Appendix~\ref{Apdx_A}. Let us define the vertical scale factor by |
---|
| 848 | $e_3=\partial_s z$ ($e_3$ is now a function of $(i,j,k,t)$ ), and the slopes in the |
---|
| 849 | (\textbf{i},\textbf{j}) directions between $s-$ and $z-$surfaces by : |
---|
[707] | 850 | \begin{equation} \label{Eq_PE_sco_slope} |
---|
| 851 | \sigma _1 =\frac{1}{e_1 }\;\left. {\frac{\partial z}{\partial i}} \right|_s |
---|
| 852 | \quad \text{, and } \quad |
---|
| 853 | \sigma _2 =\frac{1}{e_2 }\;\left. {\frac{\partial z}{\partial j}} \right|_s |
---|
| 854 | \end{equation} |
---|
[1224] | 855 | We also introduce $\omega $, a dia-surface velocity component, defined as the velocity |
---|
| 856 | relative to the moving $s$-surfaces and normal to them: |
---|
[707] | 857 | \begin{equation} \label{Eq_PE_sco_w} |
---|
[817] | 858 | \omega = w - e_3 \, \frac{\partial s}{\partial t} - \sigma _1 \,u - \sigma _2 \,v \\ |
---|
[707] | 859 | \end{equation} |
---|
| 860 | |
---|
[817] | 861 | The equations solved by the ocean model \eqref{Eq_PE} in $s-$coordinate can be written as follows: |
---|
| 862 | |
---|
| 863 | \vspace{0.5cm} |
---|
[707] | 864 | * momentum equation: |
---|
| 865 | \begin{multline} \label{Eq_PE_sco_u} |
---|
[817] | 866 | \frac{1}{e_3} \frac{\partial \left( e_3\,u \right) }{\partial t}= |
---|
| 867 | + \left( {\zeta +f} \right)\,v |
---|
| 868 | - \frac{1}{2\,e_1} \frac{\partial}{\partial i} \left( u^2+v^2 \right) |
---|
| 869 | - \frac{1}{e_3} \omega \frac{\partial u}{\partial k} \\ |
---|
| 870 | - \frac{1}{e_1} \frac{\partial}{\partial i} \left( \frac{p_s + p_h}{\rho _o} \right) |
---|
| 871 | + g\frac{\rho }{\rho _o}\sigma _1 |
---|
| 872 | + D_u^{\vect{U}} + F_u^{\vect{U}} \quad |
---|
[707] | 873 | \end{multline} |
---|
| 874 | \begin{multline} \label{Eq_PE_sco_v} |
---|
[817] | 875 | \frac{1}{e_3} \frac{\partial \left( e_3\,v \right) }{\partial t}= |
---|
| 876 | - \left( {\zeta +f} \right)\,u |
---|
| 877 | - \frac{1}{2\,e_2 }\frac{\partial }{\partial j}\left( u^2+v^2 \right) |
---|
| 878 | - \frac{1}{e_3 } \omega \frac{\partial v}{\partial k} \\ |
---|
| 879 | - \frac{1}{e_2 }\frac{\partial }{\partial j}\left( \frac{p_s+p_h }{\rho _o} \right) |
---|
| 880 | + g\frac{\rho }{\rho _o }\sigma _2 |
---|
| 881 | + D_v^{\vect{U}} + F_v^{\vect{U}} \quad |
---|
[707] | 882 | \end{multline} |
---|
[1224] | 883 | where the relative vorticity, \textit{$\zeta $}, the surface pressure gradient, and the hydrostatic |
---|
| 884 | pressure have the same expressions as in $z$-coordinates although they do not represent |
---|
| 885 | exactly the same quantities. $\omega$ is provided by the continuity equation |
---|
| 886 | (see Appendix~\ref{Apdx_A}): |
---|
[707] | 887 | |
---|
[817] | 888 | \begin{equation} \label{Eq_PE_sco_continuity} |
---|
| 889 | \frac{\partial e_3}{\partial t} + e_3 \; \chi + \frac{\partial \omega }{\partial s} = 0 |
---|
| 890 | \qquad \text{with }\;\; |
---|
[707] | 891 | \chi =\frac{1}{e_1 e_2 e_3 }\left[ {\frac{\partial \left( {e_2 e_3 \,u} |
---|
| 892 | \right)}{\partial i}+\frac{\partial \left( {e_1 e_3 \,v} \right)}{\partial |
---|
| 893 | j}} \right] |
---|
| 894 | \end{equation} |
---|
| 895 | |
---|
[817] | 896 | \vspace{0.5cm} |
---|
[707] | 897 | * tracer equations: |
---|
[817] | 898 | \begin{multline} \label{Eq_PE_sco_t} |
---|
| 899 | \frac{1}{e_3} \frac{\partial \left( e_3\,T \right) }{\partial t}= |
---|
| 900 | -\frac{1}{e_1 e_2 e_3 }\left[ {\frac{\partial \left( {e_2 e_3\,u\,T} \right)}{\partial i} |
---|
| 901 | +\frac{\partial \left( {e_1 e_3\,v\,T} \right)}{\partial j}} \right] \\ |
---|
| 902 | -\frac{1}{e_3 }\frac{\partial \left( {T\,\omega } \right)}{\partial k} + D^T + F^S \qquad |
---|
| 903 | \end{multline} |
---|
[707] | 904 | |
---|
[817] | 905 | \begin{multline} \label{Eq_PE_sco_s} |
---|
| 906 | \frac{1}{e_3} \frac{\partial \left( e_3\,S \right) }{\partial t}= |
---|
| 907 | -\frac{1}{e_1 e_2 e_3 }\left[ {\frac{\partial \left( {e_2 e_3\,u\,S} \right)}{\partial i} |
---|
| 908 | +\frac{\partial \left( {e_1 e_3\,v\,S} \right)}{\partial j}} \right] \\ |
---|
| 909 | -\frac{1}{e_3 }\frac{\partial \left( {S\,\omega } \right)}{\partial k} + D^S + F^S \qquad |
---|
| 910 | \end{multline} |
---|
[707] | 911 | |
---|
[1224] | 912 | The equation of state has the same expression as in $z$-coordinate, and similar expressions |
---|
| 913 | are used for mixing and forcing terms. |
---|
[707] | 914 | |
---|
[817] | 915 | \gmcomment{ |
---|
[707] | 916 | \colorbox{yellow}{ to be updated $= = >$} |
---|
| 917 | Add a few works on z and zps and s and underlies the differences between all of them |
---|
[817] | 918 | \colorbox{yellow}{ $< = =$ end update} } |
---|
[707] | 919 | |
---|
[1831] | 920 | |
---|
| 921 | |
---|
[707] | 922 | \newpage |
---|
| 923 | % ================================================================ |
---|
| 924 | % Subgrid Scale Physics |
---|
| 925 | % ================================================================ |
---|
| 926 | \section{Subgrid Scale Physics} |
---|
| 927 | \label{PE_zdf_ldf} |
---|
| 928 | |
---|
| 929 | The primitive equations describe the behaviour of a geophysical fluid at |
---|
| 930 | space and time scales larger than a few kilometres in the horizontal, a few |
---|
| 931 | meters in the vertical and a few minutes. They are usually solved at larger |
---|
[817] | 932 | scales: the specified grid spacing and time step of the numerical model. The |
---|
[707] | 933 | effects of smaller scale motions (coming from the advective terms in the |
---|
| 934 | Navier-Stokes equations) must be represented entirely in terms of |
---|
| 935 | large-scale patterns to close the equations. These effects appear in the |
---|
[817] | 936 | equations as the divergence of turbulent fluxes ($i.e.$ fluxes associated with |
---|
[707] | 937 | the mean correlation of small scale perturbations). Assuming a turbulent |
---|
| 938 | closure hypothesis is equivalent to choose a formulation for these fluxes. |
---|
| 939 | It is usually called the subgrid scale physics. It must be emphasized that |
---|
| 940 | this is the weakest part of the primitive equations, but also one of the |
---|
[1224] | 941 | most important for long-term simulations as small scale processes \textit{in fine} |
---|
| 942 | balance the surface input of kinetic energy and heat. |
---|
[707] | 943 | |
---|
| 944 | The control exerted by gravity on the flow induces a strong anisotropy |
---|
[1224] | 945 | between the lateral and vertical motions. Therefore subgrid-scale physics |
---|
| 946 | \textbf{D}$^{\vect{U}}$, $D^{S}$ and $D^{T}$ in \eqref{Eq_PE_dyn}, |
---|
| 947 | \eqref{Eq_PE_tra_T} and \eqref{Eq_PE_tra_S} are divided into a lateral part |
---|
| 948 | \textbf{D}$^{l \vect{U}}$, $D^{lS}$ and $D^{lT}$ and a vertical part |
---|
| 949 | \textbf{D}$^{vU}$, $D^{vS}$ and $D^{vT}$. The formulation of these terms |
---|
| 950 | and their underlying physics are briefly discussed in the next two subsections. |
---|
[707] | 951 | |
---|
| 952 | % ------------------------------------------------------------------------------------------------------------- |
---|
| 953 | % Vertical Subgrid Scale Physics |
---|
| 954 | % ------------------------------------------------------------------------------------------------------------- |
---|
| 955 | \subsection{Vertical Subgrid Scale Physics} |
---|
| 956 | \label{PE_zdf} |
---|
| 957 | |
---|
| 958 | The model resolution is always larger than the scale at which the major |
---|
[817] | 959 | sources of vertical turbulence occur (shear instability, internal wave |
---|
[707] | 960 | breaking...). Turbulent motions are thus never explicitly solved, even |
---|
| 961 | partially, but always parameterized. The vertical turbulent fluxes are |
---|
| 962 | assumed to depend linearly on the gradients of large-scale quantities (for |
---|
[1224] | 963 | example, the turbulent heat flux is given by $\overline{T'w'}=-A^{vT} \partial_z \overline T$, |
---|
| 964 | where $A^{vT}$ is an eddy coefficient). This formulation is |
---|
[707] | 965 | analogous to that of molecular diffusion and dissipation. This is quite |
---|
| 966 | clearly a necessary compromise: considering only the molecular viscosity |
---|
| 967 | acting on large scale severely underestimates the role of turbulent |
---|
| 968 | diffusion and dissipation, while an accurate consideration of the details of |
---|
| 969 | turbulent motions is simply impractical. The resulting vertical momentum and |
---|
| 970 | tracer diffusive operators are of second order: |
---|
| 971 | \begin{equation} \label{Eq_PE_zdf} |
---|
| 972 | \begin{split} |
---|
[1224] | 973 | {\vect{D}}^{v \vect{U}} &=\frac{\partial }{\partial z}\left( {A^{vm}\frac{\partial {\vect{U}}_h }{\partial z}} \right) \ , \\ |
---|
| 974 | D^{vT} &= \frac{\partial }{\partial z}\left( {A^{vT}\frac{\partial T}{\partial z}} \right) \ , |
---|
[707] | 975 | \quad |
---|
| 976 | D^{vS}=\frac{\partial }{\partial z}\left( {A^{vT}\frac{\partial S}{\partial z}} \right) |
---|
| 977 | \end{split} |
---|
| 978 | \end{equation} |
---|
[1224] | 979 | where $A^{vm}$ and $A^{vT}$ are the vertical eddy viscosity and diffusivity coefficients, |
---|
| 980 | respectively. At the sea surface and at the bottom, turbulent fluxes of momentum, heat |
---|
| 981 | and salt must be specified (see Chap.~\ref{SBC} and \ref{ZDF} and \S\ref{TRA_bbl}). |
---|
| 982 | All the vertical physics is embedded in the specification of the eddy coefficients. |
---|
| 983 | They can be assumed to be either constant, or function of the local fluid properties |
---|
| 984 | ($e.g.$ Richardson number, Brunt-Vais\"{a}l\"{a} frequency...), or computed from a |
---|
| 985 | turbulent closure model. The choices available in \NEMO are discussed in \S\ref{ZDF}). |
---|
[707] | 986 | |
---|
| 987 | % ------------------------------------------------------------------------------------------------------------- |
---|
| 988 | % Lateral Diffusive and Viscous Operators Formulation |
---|
| 989 | % ------------------------------------------------------------------------------------------------------------- |
---|
| 990 | \subsection{Lateral Diffusive and Viscous Operators Formulation} |
---|
| 991 | \label{PE_ldf} |
---|
| 992 | |
---|
| 993 | Lateral turbulence can be roughly divided into a mesoscale turbulence |
---|
[817] | 994 | associated with eddies (which can be solved explicitly if the resolution is |
---|
| 995 | sufficient since their underlying physics are included in the primitive |
---|
| 996 | equations), and a sub mesoscale turbulence which is never explicitly solved |
---|
[707] | 997 | even partially, but always parameterized. The formulation of lateral eddy |
---|
| 998 | fluxes depends on whether the mesoscale is below or above the grid-spacing |
---|
[817] | 999 | ($i.e.$ the model is eddy-resolving or not). |
---|
[707] | 1000 | |
---|
[817] | 1001 | In non-eddy-resolving configurations, the closure is similar to that used |
---|
[707] | 1002 | for the vertical physics. The lateral turbulent fluxes are assumed to depend |
---|
| 1003 | linearly on the lateral gradients of large-scale quantities. The resulting |
---|
| 1004 | lateral diffusive and dissipative operators are of second order. |
---|
| 1005 | Observations show that lateral mixing induced by mesoscale turbulence tends |
---|
[1224] | 1006 | to be along isopycnal surfaces (or more precisely neutral surfaces \cite{McDougall1987}) |
---|
| 1007 | rather than across them. |
---|
[817] | 1008 | As the slope of neutral surfaces is small in the ocean, a common |
---|
[707] | 1009 | approximation is to assume that the `lateral' direction is the horizontal, |
---|
[817] | 1010 | $i.e.$ the lateral mixing is performed along geopotential surfaces. This leads |
---|
[707] | 1011 | to a geopotential second order operator for lateral subgrid scale physics. |
---|
| 1012 | This assumption can be relaxed: the eddy-induced turbulent fluxes can be |
---|
| 1013 | better approached by assuming that they depend linearly on the gradients of |
---|
[817] | 1014 | large-scale quantities computed along neutral surfaces. In such a case, |
---|
[707] | 1015 | the diffusive operator is an isoneutral second order operator and it has |
---|
| 1016 | components in the three space directions. However, both horizontal and |
---|
[817] | 1017 | isoneutral operators have no effect on mean ($i.e.$ large scale) potential |
---|
[707] | 1018 | energy whereas potential energy is a main source of turbulence (through |
---|
| 1019 | baroclinic instabilities). \citet{Gent1990} have proposed a |
---|
[1224] | 1020 | parameterisation of mesoscale eddy-induced turbulence which associates an |
---|
[707] | 1021 | eddy-induced velocity to the isoneutral diffusion. Its mean effect is to |
---|
| 1022 | reduce the mean potential energy of the ocean. This leads to a formulation |
---|
| 1023 | of lateral subgrid-scale physics made up of an isoneutral second order |
---|
| 1024 | operator and an eddy induced advective part. In all these lateral diffusive |
---|
| 1025 | formulations, the specification of the lateral eddy coefficients remains the |
---|
[817] | 1026 | problematic point as there is no really satisfactory formulation of these |
---|
[707] | 1027 | coefficients as a function of large-scale features. |
---|
| 1028 | |
---|
| 1029 | In eddy-resolving configurations, a second order operator can be used, but |
---|
| 1030 | usually a more scale selective one (biharmonic operator) is preferred as the |
---|
| 1031 | grid-spacing is usually not small enough compared to the scale of the |
---|
| 1032 | eddies. The role devoted to the subgrid-scale physics is to dissipate the |
---|
| 1033 | energy that cascades toward the grid scale and thus ensures the stability of |
---|
[817] | 1034 | the model while not interfering with the solved mesoscale activity. Another approach |
---|
| 1035 | is becoming more and more popular: instead of specifying explicitly a sub-grid scale |
---|
[1224] | 1036 | term in the momentum and tracer time evolution equations, one uses a advective |
---|
| 1037 | scheme which is diffusive enough to maintain the model stability. It must be emphasised |
---|
[817] | 1038 | that then, all the sub-grid scale physics is in this case include in the formulation of the |
---|
| 1039 | advection scheme. |
---|
[707] | 1040 | |
---|
[1224] | 1041 | All these parameterisations of subgrid scale physics present advantages and |
---|
[817] | 1042 | drawbacks. There are not all available in \NEMO. In the $z$-coordinate |
---|
| 1043 | formulation, five options are offered for active tracers (temperature and |
---|
[707] | 1044 | salinity): second order geopotential operator, second order isoneutral |
---|
[1224] | 1045 | operator, \citet{Gent1990} parameterisation, fourth order |
---|
| 1046 | geopotential operator, and various slightly diffusive advection schemes. |
---|
| 1047 | The same options are available for momentum, except |
---|
| 1048 | \citet{Gent1990} parameterisation which only involves tracers. In the |
---|
[817] | 1049 | $s$-coordinate formulation, additional options are offered for tracers: second |
---|
[707] | 1050 | order operator acting along $s-$surfaces, and for momentum: fourth order |
---|
| 1051 | operator acting along $s-$surfaces (see \S\ref{LDF}). |
---|
| 1052 | |
---|
| 1053 | \subsubsection{lateral second order tracer diffusive operator} |
---|
| 1054 | |
---|
[817] | 1055 | The lateral second order tracer diffusive operator is defined by (see Appendix~\ref{Apdx_B}): |
---|
[707] | 1056 | \begin{equation} \label{Eq_PE_iso_tensor} |
---|
| 1057 | D^{lT}=\nabla {\rm {\bf .}}\left( {A^{lT}\;\Re \;\nabla T} \right) \qquad |
---|
| 1058 | \mbox{with}\quad \;\;\Re =\left( {{\begin{array}{*{20}c} |
---|
| 1059 | 1 \hfill & 0 \hfill & {-r_1 } \hfill \\ |
---|
| 1060 | 0 \hfill & 1 \hfill & {-r_2 } \hfill \\ |
---|
| 1061 | {-r_1 } \hfill & {-r_2 } \hfill & {r_1 ^2+r_2 ^2} \hfill \\ |
---|
| 1062 | \end{array} }} \right) |
---|
| 1063 | \end{equation} |
---|
| 1064 | where $r_1 \;\mbox{and}\;r_2 $ are the slopes between the surface along |
---|
[817] | 1065 | which the diffusive operator acts and the model level ($e. g.$ $z$- or |
---|
| 1066 | $s$-surfaces). Note that the formulation \eqref{Eq_PE_iso_tensor} is exact for the |
---|
| 1067 | rotation between geopotential and $s$-surfaces, while it is only an approximation |
---|
| 1068 | for the rotation between isoneutral and $z$- or $s$-surfaces. Indeed, in the latter |
---|
[1224] | 1069 | case, two assumptions are made to simplify \eqref{Eq_PE_iso_tensor} \citep{Cox1987}. |
---|
| 1070 | First, the horizontal contribution of the dianeutral mixing is neglected since the ratio |
---|
| 1071 | between iso and dia-neutral diffusive coefficients is known to be several orders of |
---|
| 1072 | magnitude smaller than unity. Second, the two isoneutral directions of diffusion are |
---|
| 1073 | assumed to be independent since the slopes are generally less than $10^{-2}$ in the |
---|
| 1074 | ocean (see Appendix~\ref{Apdx_B}). |
---|
[707] | 1075 | |
---|
| 1076 | For \textit{geopotential} diffusion, $r_1$ and $r_2 $ are the slopes between the |
---|
[1224] | 1077 | geopotential and computational surfaces: in $z$-coordinates they are zero |
---|
| 1078 | ($r_1 = r_2 = 0$) while in $s$-coordinate (including $\textit{z*}$ case) they are |
---|
| 1079 | equal to $\sigma _1$ and $\sigma _2$, respectively (see \eqref{Eq_PE_sco_slope} ). |
---|
[707] | 1080 | |
---|
[1224] | 1081 | For \textit{isoneutral} diffusion $r_1$ and $r_2$ are the slopes between the isoneutral |
---|
| 1082 | and computational surfaces. Therefore, they have a same expression in $z$- and $s$-coordinates: |
---|
[707] | 1083 | \begin{equation} \label{Eq_PE_iso_slopes} |
---|
| 1084 | r_1 =\frac{e_3 }{e_1 } \left( {\frac{\partial \rho }{\partial i}} \right) |
---|
| 1085 | \left( {\frac{\partial \rho }{\partial k}} \right)^{-1} \ , \quad |
---|
| 1086 | r_1 =\frac{e_3 }{e_1 } \left( {\frac{\partial \rho }{\partial i}} \right) |
---|
| 1087 | \left( {\frac{\partial \rho }{\partial k}} \right)^{-1} |
---|
| 1088 | \end{equation} |
---|
| 1089 | |
---|
[1224] | 1090 | When the \textit{Eddy Induced Velocity} parametrisation (eiv) \citep{Gent1990} is used, |
---|
| 1091 | an additional tracer advection is introduced in combination with the isoneutral diffusion of tracers: |
---|
[707] | 1092 | \begin{equation} \label{Eq_PE_iso+eiv} |
---|
| 1093 | D^{lT}=\nabla \cdot \left( {A^{lT}\;\Re \;\nabla T} \right) |
---|
| 1094 | +\nabla \cdot \left( {{\vect{U}}^\ast \,T} \right) |
---|
| 1095 | \end{equation} |
---|
[1224] | 1096 | where ${\vect{U}}^\ast =\left( {u^\ast ,v^\ast ,w^\ast } \right)$ is a non-divergent, |
---|
| 1097 | eddy-induced transport velocity. This velocity field is defined by: |
---|
[707] | 1098 | \begin{equation} \label{Eq_PE_eiv} |
---|
| 1099 | \begin{split} |
---|
| 1100 | u^\ast &= +\frac{1}{e_3 }\frac{\partial }{\partial k}\left[ {A^{eiv}\;\tilde{r}_1 } \right] \\ |
---|
| 1101 | v^\ast &= +\frac{1}{e_3 }\frac{\partial }{\partial k}\left[ {A^{eiv}\;\tilde{r}_2 } \right] \\ |
---|
| 1102 | w^\ast &= -\frac{1}{e_1 e_2 }\left[ |
---|
| 1103 | \frac{\partial }{\partial i}\left( {A^{eiv}\;e_2\,\tilde{r}_1 } \right) |
---|
| 1104 | +\frac{\partial }{\partial j}\left( {A^{eiv}\;e_1\,\tilde{r}_2 } \right) \right] |
---|
| 1105 | \end{split} |
---|
| 1106 | \end{equation} |
---|
[1224] | 1107 | where $A^{eiv}$ is the eddy induced velocity coefficient (or equivalently the isoneutral |
---|
| 1108 | thickness diffusivity coefficient), and $\tilde{r}_1$ and $\tilde{r}_2$ are the slopes |
---|
| 1109 | between isoneutral and \emph{geopotential} surfaces and thus depends on the coordinate |
---|
| 1110 | considered: |
---|
[707] | 1111 | \begin{align} \label{Eq_PE_slopes_eiv} |
---|
| 1112 | \tilde{r}_n = \begin{cases} |
---|
[817] | 1113 | r_n & \text{in $z$-coordinate} \\ |
---|
| 1114 | r_n + \sigma_n & \text{in \textit{z*} and $s$-coordinates} |
---|
[707] | 1115 | \end{cases} |
---|
| 1116 | \quad \text{where } n=1,2 |
---|
| 1117 | \end{align} |
---|
| 1118 | |
---|
[1224] | 1119 | The normal component of the eddy induced velocity is zero at all the boundaries. |
---|
| 1120 | This can be achieved in a model by tapering either the eddy coefficient or the slopes |
---|
| 1121 | to zero in the vicinity of the boundaries. The latter strategy is used in \NEMO (cf. Chap.~\ref{LDF}). |
---|
[707] | 1122 | |
---|
| 1123 | \subsubsection{lateral fourth order tracer diffusive operator} |
---|
| 1124 | |
---|
| 1125 | The lateral fourth order tracer diffusive operator is defined by: |
---|
| 1126 | \begin{equation} \label{Eq_PE_bilapT} |
---|
| 1127 | D^{lT}=\Delta \left( {A^{lT}\;\Delta T} \right) |
---|
| 1128 | \qquad \text{where} \ D^{lT}=\Delta \left( {A^{lT}\;\Delta T} \right) |
---|
| 1129 | \end{equation} |
---|
| 1130 | |
---|
[1224] | 1131 | It is the second order operator given by \eqref{Eq_PE_iso_tensor} applied twice with |
---|
| 1132 | the eddy diffusion coefficient correctly placed. |
---|
[707] | 1133 | |
---|
[817] | 1134 | |
---|
[707] | 1135 | \subsubsection{lateral second order momentum diffusive operator} |
---|
| 1136 | |
---|
[817] | 1137 | The second order momentum diffusive operator along $z$- or $s$-surfaces is found by |
---|
| 1138 | applying \eqref{Eq_PE_lap_vector} to the horizontal velocity vector (see Appendix~\ref{Apdx_B}): |
---|
[707] | 1139 | \begin{equation} \label{Eq_PE_lapU} |
---|
| 1140 | \begin{split} |
---|
| 1141 | {\rm {\bf D}}^{l{\rm {\bf U}}} |
---|
| 1142 | &= \quad \ \nabla _h \left( {A^{lm}\chi } \right) |
---|
| 1143 | \ - \ \nabla _h \times \left( {A^{lm}\,\zeta \;{\rm {\bf k}}} \right) \\ |
---|
| 1144 | &= \left( \begin{aligned} |
---|
| 1145 | \frac{1}{e_1 } \frac{\partial \left( A^{lm} \chi \right)}{\partial i} |
---|
| 1146 | &-\frac{1}{e_2 e_3}\frac{\partial \left( {A^{lm} \;e_3 \zeta} \right)}{\partial j} \\ |
---|
| 1147 | \frac{1}{e_2 }\frac{\partial \left( {A^{lm} \chi } \right)}{\partial j} |
---|
| 1148 | &+\frac{1}{e_1 e_3}\frac{\partial \left( {A^{lm} \;e_3 \zeta} \right)}{\partial i} |
---|
| 1149 | \end{aligned} \right) |
---|
| 1150 | \end{split} |
---|
| 1151 | \end{equation} |
---|
| 1152 | |
---|
| 1153 | Such a formulation ensures a complete separation between the vorticity and |
---|
[817] | 1154 | horizontal divergence fields (see Appendix~\ref{Apdx_C}). Unfortunately, it is not |
---|
[707] | 1155 | available for geopotential diffusion in $s-$coordinates and for isoneutral |
---|
[1224] | 1156 | diffusion in both $z$- and $s$-coordinates ($i.e.$ when a rotation is required). |
---|
| 1157 | In these two cases, the $u$ and $v-$fields are considered as independent scalar |
---|
| 1158 | fields, so that the diffusive operator is given by: |
---|
[707] | 1159 | \begin{equation} \label{Eq_PE_lapU_iso} |
---|
| 1160 | \begin{split} |
---|
| 1161 | D_u^{l{\rm {\bf U}}} &= \nabla .\left( {\Re \;\nabla u} \right) \\ |
---|
| 1162 | D_v^{l{\rm {\bf U}}} &= \nabla .\left( {\Re \;\nabla v} \right) |
---|
| 1163 | \end{split} |
---|
| 1164 | \end{equation} |
---|
[1224] | 1165 | where $\Re$ is given by \eqref{Eq_PE_iso_tensor}. It is the same expression as |
---|
| 1166 | those used for diffusive operator on tracers. It must be emphasised that such a |
---|
| 1167 | formulation is only exact in a Cartesian coordinate system, $i.e.$ on a $f-$ or |
---|
| 1168 | $\beta-$plane, not on the sphere. It is also a very good approximation in vicinity |
---|
| 1169 | of the Equator in a geographical coordinate system \citep{Lengaigne_al_JGR03}. |
---|
[707] | 1170 | |
---|
| 1171 | \subsubsection{lateral fourth order momentum diffusive operator} |
---|
| 1172 | |
---|
[1224] | 1173 | As for tracers, the fourth order momentum diffusive operator along $z$ or $s$-surfaces |
---|
| 1174 | is a re-entering second order operator \eqref{Eq_PE_lapU} or \eqref{Eq_PE_lapU} |
---|
| 1175 | with the eddy viscosity coefficient correctly placed: |
---|
[707] | 1176 | |
---|
[817] | 1177 | geopotential diffusion in $z$-coordinate: |
---|
[707] | 1178 | \begin{equation} \label{Eq_PE_bilapU} |
---|
| 1179 | \begin{split} |
---|
| 1180 | {\rm {\bf D}}^{l{\rm {\bf U}}} &=\nabla _h \left\{ {\;\nabla _h {\rm {\bf |
---|
| 1181 | .}}\left[ {A^{lm}\,\nabla _h \left( \chi \right)} \right]\;} |
---|
| 1182 | \right\}\; \\ |
---|
| 1183 | &+\nabla _h \times \left\{ {\;{\rm {\bf k}}\cdot \nabla \times |
---|
| 1184 | \left[ {A^{lm}\,\nabla _h \times \left( {\zeta \;{\rm {\bf k}}} \right)} |
---|
| 1185 | \right]\;} \right\} |
---|
| 1186 | \end{split} |
---|
| 1187 | \end{equation} |
---|
| 1188 | |
---|
[817] | 1189 | \gmcomment{ change the position of the coefficient, both here and in the code} |
---|
| 1190 | |
---|
| 1191 | geopotential diffusion in $s$-coordinate: |
---|
[707] | 1192 | \begin{equation} \label{Eq_bilapU_iso} |
---|
| 1193 | \left\{ \begin{aligned} |
---|
| 1194 | D_u^{l{\rm {\bf U}}} =\Delta \left( {A^{lm}\;\Delta u} \right) \\ |
---|
| 1195 | D_v^{l{\rm {\bf U}}} =\Delta \left( {A^{lm}\;\Delta v} \right) |
---|
| 1196 | \end{aligned} \right. |
---|
| 1197 | \quad \text{where} \quad |
---|
| 1198 | \Delta \left( \bullet \right) = \nabla \cdot \left( \Re \nabla(\bullet) \right) |
---|
| 1199 | \end{equation} |
---|
| 1200 | |
---|