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NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex
r10442 r10502 3 3 \begin{document} 4 4 % ================================================================ 5 % Chapter 2 Space and Time Domain (DOM)5 % Chapter 2 ——— Space and Time Domain (DOM) 6 6 % ================================================================ 7 7 \chapter{Space Domain (DOM)} … … 40 40 \begin{figure}[!tb] 41 41 \begin{center} 42 \includegraphics[ width=0.90\textwidth]{Fig_cell}42 \includegraphics[]{Fig_cell} 43 43 \caption{ 44 44 \protect\label{fig:cell} … … 46 46 $t$ indicates scalar points where temperature, salinity, density, pressure and 47 47 horizontal divergence are defined. 48 ($u$,$v$,$w$) indicates vector points,49 and $f$ indicates vorticity points where both relative and planetary vorticities are defined48 $(u,v,w)$ indicates vector points, and $f$ indicates vorticity points where both relative and 49 planetary vorticities are defined. 50 50 } 51 51 \end{center} … … 64 64 the barotropic stream function $\psi$ is defined at horizontal points overlying the $\zeta$ and $f$-points. 65 65 66 The ocean mesh (\ie the position of all the scalar and vector points) is defined by 67 the transformation that gives ($\lambda$ ,$\varphi$ ,$z$)as a function of $(i,j,k)$.66 The ocean mesh (\ie the position of all the scalar and vector points) is defined by the transformation that 67 gives $(\lambda,\varphi,z)$ as a function of $(i,j,k)$. 68 68 The grid-points are located at integer or integer and a half value of $(i,j,k)$ as indicated on \autoref{tab:cell}. 69 69 In all the following, subscripts $u$, $v$, $w$, $f$, $uw$, $vw$ or $fw$ indicate the position of 70 70 the grid-point where the scale factors are defined. 71 71 Each scale factor is defined as the local analytical value provided by \autoref{eq:scale_factors}. 72 As a result, 73 the mesh on which partial derivatives $\frac{\partial}{\partial \lambda}, \frac{\partial}{\partial \varphi}$, 74 and $\frac{\partial}{\partial z} $ are evaluated is a uniform mesh with a grid size of unity. 75 Discrete partial derivatives are formulated by the traditional, 76 centred second order finite difference approximation while 77 the scale factors are chosen equal to their local analytical value. 72 As a result, the mesh on which partial derivatives $\pd[]{\lambda}$, $\pd[]{\varphi}$ and 73 $\pd[]{z}$ are evaluated in a uniform mesh with a grid size of unity. 74 Discrete partial derivatives are formulated by the traditional, centred second order finite difference approximation 75 while the scale factors are chosen equal to their local analytical value. 78 76 An important point here is that the partial derivative of the scale factors must be evaluated by 79 77 centred finite difference approximation, not from their analytical expression. 80 This preserves the symmetry of the discrete set of equations and 81 the refore satisfies many of thecontinuous properties (see \autoref{apdx:C}).78 This preserves the symmetry of the discrete set of equations and therefore satisfies many of 79 the continuous properties (see \autoref{apdx:C}). 82 80 A similar, related remark can be made about the domain size: 83 81 when needed, an area, volume, or the total ocean depth must be evaluated as the sum of the relevant scale factors 84 (see \autoref{eq:DOM_bar} )in the next section).82 (see \autoref{eq:DOM_bar} in the next section). 85 83 86 84 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> … … 89 87 \begin{tabular}{|p{46pt}|p{56pt}|p{56pt}|p{56pt}|} 90 88 \hline 91 T &$i$ & $j$ & $k$ \\ \hline 92 u & $i+1/2$ & $j$ & $k$ \\ \hline 93 v & $i$ & $j+1/2$ & $k$ \\ \hline 94 w & $i$ & $j$ & $k+1/2$ \\ \hline 95 f & $i+1/2$ & $j+1/2$ & $k$ \\ \hline 96 uw & $i+1/2$ & $j$ & $k+1/2$ \\ \hline 97 vw & $i$ & $j+1/2$ & $k+1/2$ \\ \hline 98 fw & $i+1/2$ & $j+1/2$ & $k+1/2$ \\ \hline 89 T & $i $ & $j $ & $k $ \\ 90 \hline 91 u & $i + 1/2$ & $j $ & $k $ \\ 92 \hline 93 v & $i $ & $j + 1/2$ & $k $ \\ 94 \hline 95 w & $i $ & $j $ & $k + 1/2$ \\ 96 \hline 97 f & $i + 1/2$ & $j + 1/2$ & $k $ \\ 98 \hline 99 uw & $i + 1/2$ & $j $ & $k + 1/2$ \\ 100 \hline 101 vw & $i $ & $j + 1/2$ & $k + 1/2$ \\ 102 \hline 103 fw & $i + 1/2$ & $j + 1/2$ & $k + 1/2$ \\ 104 \hline 99 105 \end{tabular} 100 106 \caption{ 101 107 \protect\label{tab:cell} 102 108 Location of grid-points as a function of integer or integer and a half value of the column, line or level. 103 This indexing is only used for the writing of the semi -discrete equation.109 This indexing is only used for the writing of the semi -discrete equation. 104 110 In the code, the indexing uses integer values only and has a reverse direction in the vertical 105 111 (see \autoref{subsec:DOM_Num_Index}) … … 115 121 \label{subsec:DOM_operators} 116 122 117 Given the values of a variable $q$ at adjacent points, 118 the differencing and averaging operators at themidpoint between them are:119 \ [123 Given the values of a variable $q$ at adjacent points, the differencing and averaging operators at 124 the midpoint between them are: 125 \begin{alignat*}{2} 120 126 % \label{eq:di_mi} 121 \begin{split} 122 \delta_i [q] &= \ \ q(i+1/2) - q(i-1/2) \\ 123 \overline q^{\,i} &= \left\{ q(i+1/2) + q(i-1/2) \right\} \; / \; 2 124 \end{split} 125 \] 126 127 Similar operators are defined with respect to $i+1/2$, $j$, $j+1/2$, $k$, and $k+1/2$. 127 \delta_i [q] &= & &q (i + 1/2) - q (i - 1/2) \\ 128 \overline q^{\, i} &= &\big\{ &q (i + 1/2) + q (i - 1/2) \big\} / 2 129 \end{alignat*} 130 131 Similar operators are defined with respect to $i + 1/2$, $j$, $j + 1/2$, $k$, and $k + 1/2$. 128 132 Following \autoref{eq:PE_grad} and \autoref{eq:PE_lap}, the gradient of a variable $q$ defined at 129 133 a $t$-point has its three components defined at $u$-, $v$- and $w$-points while 130 its Laplaci en is defined at $t$-point.131 These operators have the following discrete forms in the curvilinear $s$-coordinate system:134 its Laplacian is defined at $t$-point. 135 These operators have the following discrete forms in the curvilinear $s$-coordinates system: 132 136 \[ 133 137 % \label{eq:DOM_grad} 134 \nabla q \equiv \frac{1}{e_{1u} } \delta_{i+1/2 } [q] \;\,\mathbf{i}135 + \frac{1}{e_{2v} } \delta_{j+1/2 } [q] \;\,\mathbf{j}136 + \frac{1}{e_{3w}} \delta_{k+1/2} [q] \;\,\mathbf{k}138 \nabla q \equiv \frac{1}{e_{1u}} \delta_{i + 1/2} [q] \; \, \vect i 139 + \frac{1}{e_{2v}} \delta_{j + 1/2} [q] \; \, \vect j 140 + \frac{1}{e_{3w}} \delta_{k + 1/2} [q] \; \, \vect k 137 141 \] 138 142 \begin{multline*} 139 143 % \label{eq:DOM_lap} 140 \Delta q\equiv \frac{1}{e_{1t}\,e_{2t}\,e_{3t} } 141 \;\left( \delta_i \left[ \frac{e_{2u}\,e_{3u}} {e_{1u}} \;\delta_{i+1/2} [q] \right] 142 + \delta_j \left[ \frac{e_{1v}\,e_{3v}} {e_{2v}} \;\delta_{j+1/2} [q] \right] \; \right) \\ 143 +\frac{1}{e_{3t}} \delta_k \left[ \frac{1}{e_{3w} } \;\delta_{k+1/2} [q] \right] 144 \Delta q \equiv \frac{1}{e_{1t} \, e_{2t} \, e_{3t}} 145 \; \lt[ \delta_i \lt( \frac{e_{2u} \, e_{3u}}{e_{1u}} \; \delta_{i + 1/2} [q] \rt) 146 + \delta_j \lt( \frac{e_{1v} \, e_{3v}}{e_{2v}} \; \delta_{j + 1/2} [q] \rt) \; \rt] \\ 147 + \frac{1}{e_{3t}} 148 \delta_k \lt[ \frac{1 }{e_{3w}} \; \delta_{k + 1/2} [q] \rt] 144 149 \end{multline*} 145 150 146 Following \autoref{eq:PE_curl} and \autoref{eq:PE_div}, a vector ${\rm {\bf A}}=\left( a_1,a_2,a_3\right)$ 147 defined at vector points $(u,v,w)$ has its three curl components defined at $vw$-, $uw$, and $f$-points, 148 and its divergence defined at $t$-points: 149 \begin{align*} 150 % \label{eq:DOM_curl} 151 \nabla \times {\rm{\bf A}}\equiv & 152 \frac{1}{e_{2v}\,e_{3vw} } \ \left( \delta_{j +1/2} \left[e_{3w}\,a_3 \right] -\delta_{k+1/2} \left[e_{2v} \,a_2 \right] \right) &\ \mathbf{i} \\ 153 +& \frac{1}{e_{2u}\,e_{3uw}} \ \left( \delta_{k+1/2} \left[e_{1u}\,a_1 \right] -\delta_{i +1/2} \left[e_{3w}\,a_3 \right] \right) &\ \mathbf{j} \\ 154 +& \frac{1}{e_{1f} \,e_{2f} } \ \left( \delta_{i +1/2} \left[e_{2v}\,a_2 \right] -\delta_{j +1/2} \left[e_{1u}\,a_1 \right] \right) &\ \mathbf{k} 155 \end{align*} 156 \begin{align*} 157 % \label{eq:DOM_div} 158 \nabla \cdot \rm{\bf A} \equiv 159 \frac{1}{e_{1t}\,e_{2t}\,e_{3t}} \left( \delta_i \left[e_{2u}\,e_{3u}\,a_1 \right] 160 +\delta_j \left[e_{1v}\,e_{3v}\,a_2 \right] \right)+\frac{1}{e_{3t} }\delta_k \left[a_3 \right] 161 \end{align*} 151 Following \autoref{eq:PE_curl} and \autoref{eq:PE_div}, a vector $\vect A = (a_1,a_2,a_3)$ defined at 152 vector points $(u,v,w)$ has its three curl components defined at $vw$-, $uw$, and $f$-points, and 153 its divergence defined at $t$-points: 154 \begin{multline} 155 % \label{eq:DOM_curl} 156 \nabla \times \vect A \equiv \frac{1}{e_{2v} \, e_{3vw}} 157 \Big[ \delta_{j + 1/2} (e_{3w} \, a_3) 158 - \delta_{k + 1/2} (e_{2v} \, a_2) \Big] \vect i \\ 159 + \frac{1}{e_{2u} \, e_{3uw}} 160 \Big[ \delta_{k + 1/2} (e_{1u} \, a_1) 161 - \delta_{i + 1/2} (e_{3w} \, a_3) \Big] \vect j \\ 162 + \frac{1}{e_{1f} \, e_{2f}} 163 \Big[ \delta_{i + 1/2} (e_{2v} \, a_2) 164 - \delta_{j + 1/2} (e_{1u} \, a_1) \Big] \vect k 165 \end{multline} 166 \begin{equation} 167 % \label{eq:DOM_div} 168 \nabla \cdot \vect A \equiv \frac{1}{e_{1t} \, e_{2t} \, e_{3t}} 169 \Big[ \delta_i (e_{2u} \, e_{3u} \, a_1) + \delta_j (e_{1v} \, e_{3v} \, a_2) \Big] 170 + \frac{1}{e_{3t}} \delta_k (a_3) 171 \end{equation} 162 172 163 173 The vertical average over the whole water column denoted by an overbar becomes for a quantity $q$ which 164 is a masked field ( \ieequal to zero inside solid area):174 is a masked field (i.e. equal to zero inside solid area): 165 175 \begin{equation} 166 176 \label{eq:DOM_bar} 167 \bar q = \frac{1}{H} \int_{k^b}^{k^o} {q\;e_{3q} \,dk} 168 \equiv \frac{1}{H_q }\sum\limits_k {q\;e_{3q} } 177 \bar q = \frac{1}{H} \int_{k^b}^{k^o} q \; e_{3q} \, dk \equiv \frac{1}{H_q} \sum \limits_k q \; e_{3q} 169 178 \end{equation} 170 179 where $H_q$ is the ocean depth, which is the masked sum of the vertical scale factors at $q$ points, 171 $k^b$ and $k^o$ are the bottom and surface $k$-indices, 172 and the symbol $k^o$ refers to a summation over all grid points of the same type in the direction indicated by 173 the subscript (here $k$). 180 $k^b$ and $k^o$ are the bottom and surface $k$-indices, and the symbol $k^o$ refers to a summation over 181 all grid points of the same type in the direction indicated by the subscript (here $k$). 174 182 175 183 In continuous form, the following properties are satisfied: 176 \begin{ equation}184 \begin{gather} 177 185 \label{eq:DOM_curl_grad} 178 \nabla \times \nabla q ={\rm {\bf {0}}} 179 \end{equation} 180 \begin{equation} 186 \nabla \times \nabla q = \vect 0 \\ 181 187 \label{eq:DOM_div_curl} 182 \nabla \cdot \left( {\nabla \times {\rm {\bf A}}} \right)=0183 \end{ equation}188 \nabla \cdot (\nabla \times \vect A) = 0 189 \end{gather} 184 190 185 191 It is straightforward to demonstrate that these properties are verified locally in discrete form as soon as 186 the scalar $q$ is taken at $t$-points and 187 the vector \textbf{A} has its components defined atvector points $(u,v,w)$.192 the scalar $q$ is taken at $t$-points and the vector $\vect A$ has its components defined at 193 vector points $(u,v,w)$. 188 194 189 195 Let $a$ and $b$ be two fields defined on the mesh, with value zero inside continental area. 190 Using integration by parts it can be shown that 191 the differencing operators ($\delta_i$, $\delta_j$ and $\delta_k$) are skew-symmetric linear operators, 192 and further that the averaging operators $\overline{\,\cdot\,}^{\,i}$, $\overline{\,\cdot\,}^{\,k}$ and 193 $\overline{\,\cdot\,}^{\,k}$) are symmetric linear operators, \ie 194 \begin{align} 196 Using integration by parts it can be shown that the differencing operators ($\delta_i$, $\delta_j$ and $\delta_k$) 197 are skew-symmetric linear operators, and further that the averaging operators $\overline{\cdots}^{\, i}$, 198 $\overline{\cdots}^{\, j}$ and $\overline{\cdots}^{\, k}$) are symmetric linear operators, \ie 199 \begin{alignat}{4} 195 200 \label{eq:DOM_di_adj} 196 \sum\limits_i { a_i \;\delta_i \left[ b \right]} 197 &\equiv -\sum\limits_i {\delta_{i+1/2} \left[ a \right]\;b_{i+1/2} } \\ 201 &\sum \limits_i a_i \; \delta_i [b] &\equiv &- &&\sum \limits_i \delta _{ i + 1/2} [a] &b_{i + 1/2} \\ 198 202 \label{eq:DOM_mi_adj} 199 \sum\limits_i { a_i \;\overline b^{\,i}} 200 & \equiv \quad \sum\limits_i {\overline a ^{\,i+1/2}\;b_{i+1/2} } 201 \end{align} 202 203 In other words, the adjoint of the differencing and averaging operators are $\delta_i^*=\delta_{i+1/2}$ and 204 ${(\overline{\,\cdot \,}^{\,i})}^*= \overline{\,\cdot\,}^{\,i+1/2}$, respectively. 203 &\sum \limits_i a_i \; \overline b^{\, i} &\equiv & &&\sum \limits_i \overline a ^{\, i + 1/2} &b_{i + 1/2} 204 \end{alignat} 205 206 In other words, the adjoint of the differencing and averaging operators are $\delta_i^* = \delta_{i + 1/2}$ and 207 $(\overline{\cdots}^{\, i})^* = \overline{\cdots}^{\, i + 1/2}$, respectively. 205 208 These two properties will be used extensively in the \autoref{apdx:C} to 206 209 demonstrate integral conservative properties of the discrete formulation chosen. … … 215 218 \begin{figure}[!tb] 216 219 \begin{center} 217 \includegraphics[ width=0.90\textwidth]{Fig_index_hor}220 \includegraphics[]{Fig_index_hor} 218 221 \caption{ 219 222 \protect\label{fig:index_hor} … … 230 233 Therefore a specific integer indexing must be defined for points other than $t$-points 231 234 (\ie velocity and vorticity grid-points). 232 Furthermore, the direction of the vertical indexing has been changed so that the surface level is at $k =1$.235 Furthermore, the direction of the vertical indexing has been changed so that the surface level is at $k = 1$. 233 236 234 237 % ----------------------------------- … … 250 253 \label{subsec:DOM_Num_Index_vertical} 251 254 252 In the vertical, the chosen indexing requires special attention since 253 the $k$-axis is re-orientated downward in the \fortran code compared to254 the indexing used in the semi-discrete equations andgiven in \autoref{subsec:DOM_cell}.255 The sea surface corresponds to the $w$-level $k =1$ which is the same index as $t$-level just below255 In the vertical, the chosen indexing requires special attention since the $k$-axis is re-orientated downward in 256 the \fortran code compared to the indexing used in the semi -discrete equations and 257 given in \autoref{subsec:DOM_cell}. 258 The sea surface corresponds to the $w$-level $k = 1$ which is the same index as $t$-level just below 256 259 (\autoref{fig:index_vert}). 257 The last $w$-level ($k =jpk$) either corresponds to the ocean floor or is inside the bathymetry while260 The last $w$-level ($k = jpk$) either corresponds to the ocean floor or is inside the bathymetry while 258 261 the last $t$-level is always inside the bathymetry (\autoref{fig:index_vert}). 259 262 Note that for an increasing $k$ index, a $w$-point and the $t$-point just below have the same $k$ index, … … 262 265 have the same $i$ or $j$ index 263 266 (compare the dashed area in \autoref{fig:index_hor} and \autoref{fig:index_vert}). 264 Since the scale factors are chosen to be strictly positive, a \emph{minus sign} appears in the \fortran 265 code \emph{before all the vertical derivatives} of the discrete equations given in this documentation. 267 Since the scale factors are chosen to be strictly positive, 268 a \textit{minus sign} appears in the \fortran code \textit{before all the vertical derivatives} of 269 the discrete equations given in this documentation. 266 270 267 271 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 268 272 \begin{figure}[!pt] 269 273 \begin{center} 270 \includegraphics[ width=.90\textwidth]{Fig_index_vert}274 \includegraphics[]{Fig_index_vert} 271 275 \caption{ 272 276 \protect\label{fig:index_vert} … … 287 291 The total size of the computational domain is set by the parameters \np{jpiglo}, 288 292 \np{jpjglo} and \np{jpkglo} in the $i$, $j$ and $k$ directions respectively. 289 %%%290 %%%291 %%%292 293 Parameters $jpi$ and $jpj$ refer to the size of each processor subdomain when 293 294 the code is run in parallel using domain decomposition (\key{mpp\_mpi} defined, … … 299 300 \section{Needed fields} 300 301 \label{sec:DOM_fields} 301 The ocean mesh (\ie the position of all the scalar and vector points) is defined by the transformation that gives $(\lambda,\varphi,z)$ as a function of $(i,j,k)$. 302 The ocean mesh (\ie the position of all the scalar and vector points) is defined by the transformation that 303 gives $(\lambda,\varphi,z)$ as a function of $(i,j,k)$. 302 304 The grid-points are located at integer or integer and a half values of as indicated in \autoref{tab:cell}. 303 305 The associated scale factors are defined using the analytical first derivative of the transformation 304 306 \autoref{eq:scale_factors}. 305 Necessary fields for configuration definition are: \\ 306 Geographic position : 307 308 longitude: glamt, glamu, glamv and glamf (at T, U, V and F point) 309 310 latitude: gphit, gphiu, gphiv and gphif (at T, U, V and F point)\\ 311 Coriolis parameter (if domain not on the sphere): 312 313 ff\_f and ff\_t (at T and F point)\\ 314 Scale factors : 307 Necessary fields for configuration definition are: 308 309 \begin{itemize} 310 \item 311 Geographic position: 312 longitude with \texttt{glamt}, \texttt{glamu}, \texttt{glamv}, \texttt{glamf} and 313 latitude with \texttt{gphit}, \texttt{gphiu}, \texttt{gphiv}, \texttt{gphif} 314 (all respectively at T, U, V and F point) 315 \item 316 Coriolis parameter (if domain not on the sphere): \texttt{ff\_f} and \texttt{ff\_t} 317 (at T and F point) 318 \item 319 Scale factors: 320 \texttt{e1t}, \texttt{e1u}, \texttt{e1v} and \texttt{e1f} (on i direction), 321 \texttt{e2t}, \texttt{e2u}, \texttt{e2v} and \texttt{e2f} (on j direction) and 322 \texttt{ie1e2u\_v}, \texttt{e1e2u}, \texttt{e1e2v}. \\ 323 \texttt{e1e2u}, \texttt{e1e2v} are u and v surfaces (if gridsize reduction in some straits), 324 \texttt{ie1e2u\_v} is to flag set u and v surfaces are neither read nor computed. 325 \end{itemize} 315 326 316 e1t, e1u, e1v and e1f (on i direction), 317 318 e2t, e2u, e2v and e2f (on j direction) and 319 320 ie1e2u\_v, e1e2u , e1e2v 321 322 e1e2u , e1e2v are u and v surfaces (if gridsize reduction in some straits)\\ 323 ie1e2u\_v is a flag to flag set u and v surfaces are neither read nor computed.\\ 324 325 These fields can be read in an domain input file which name is setted in 326 \np{cn\_domcfg} parameter specified in \ngn{namcfg}. 327 These fields can be read in an domain input file which name is setted in \np{cn\_domcfg} parameter specified in 328 \ngn{namcfg}. 327 329 328 330 \nlst{namcfg} 329 or they can be defined in an analytical way in MY\_SRC directory of the configuration. 331 332 Or they can be defined in an analytical way in \path{MY_SRC} directory of the configuration. 330 333 For Reference Configurations of NEMO input domain files are supplied by NEMO System Team. 331 For analytical definition of input fields two routines are supplied: \mdl{us erdef\_hgr} and \mdl{userdef\_zgr}.332 They are an example of GYRE configuration parameters, and they are available in NEMO/OPA\_SRC/USRdirectory,333 they provide the horizontal and vertical mesh. 334 For analytical definition of input fields two routines are supplied: \mdl{usrdef\_hgr} and \mdl{usrdef\_zgr}. 335 They are an example of GYRE configuration parameters, and they are available in \path{src/OCE/USR} directory, 336 they provide the horizontal and vertical mesh. 334 337 % ------------------------------------------------------------------------------------------------------------- 335 338 % Needed fields … … 366 369 ($i$ and $j$, respectively) (geographical configuration of the mesh), 367 370 the horizontal mesh definition reduces to define the wanted $\lambda(i)$, $\varphi(j)$, 368 and their derivatives $\lambda'(i) $ $\varphi'(j)$ in the \mdl{domhgr} module.371 and their derivatives $\lambda'(i) \ \varphi'(j)$ in the \mdl{domhgr} module. 369 372 The model computes the grid-point positions and scale factors in the horizontal plane as follows: 370 \begin{flalign*} 371 \lambda_t &\equiv \text{glamt}= \lambda(i) & \varphi_t &\equiv \text{gphit} = \varphi(j)\\ 372 \lambda_u &\equiv \text{glamu}= \lambda(i+1/2)& \varphi_u &\equiv \text{gphiu}= \varphi(j)\\ 373 \lambda_v &\equiv \text{glamv}= \lambda(i) & \varphi_v &\equiv \text{gphiv} = \varphi(j+1/2)\\ 374 \lambda_f &\equiv \text{glamf }= \lambda(i+1/2)& \varphi_f &\equiv \text{gphif }= \varphi(j+1/2) 375 \end{flalign*} 376 \begin{flalign*} 377 e_{1t} &\equiv \text{e1t} = r_a |\lambda'(i) \; \cos\varphi(j) |& 378 e_{2t} &\equiv \text{e2t} = r_a |\varphi'(j)| \\ 379 e_{1u} &\equiv \text{e1t} = r_a |\lambda'(i+1/2) \; \cos\varphi(j) |& 380 e_{2u} &\equiv \text{e2t} = r_a |\varphi'(j)|\\ 381 e_{1v} &\equiv \text{e1t} = r_a |\lambda'(i) \; \cos\varphi(j+1/2) |& 382 e_{2v} &\equiv \text{e2t} = r_a |\varphi'(j+1/2)|\\ 383 e_{1f} &\equiv \text{e1t} = r_a |\lambda'(i+1/2)\; \cos\varphi(j+1/2) |& 384 e_{2f} &\equiv \text{e2t} = r_a |\varphi'(j+1/2)| 385 \end{flalign*} 373 \begin{align*} 374 \lambda_t &\equiv \text{glamt} = \lambda (i ) 375 &\varphi_t &\equiv \text{gphit} = \varphi (j ) \\ 376 \lambda_u &\equiv \text{glamu} = \lambda (i + 1/2) 377 &\varphi_u &\equiv \text{gphiu} = \varphi (j ) \\ 378 \lambda_v &\equiv \text{glamv} = \lambda (i ) 379 &\varphi_v &\equiv \text{gphiv} = \varphi (j + 1/2) \\ 380 \lambda_f &\equiv \text{glamf} = \lambda (i + 1/2) 381 &\varphi_f &\equiv \text{gphif} = \varphi (j + 1/2) \\ 382 e_{1t} &\equiv \text{e1t} = r_a |\lambda'(i ) \; \cos\varphi(j ) | 383 &e_{2t} &\equiv \text{e2t} = r_a |\varphi'(j ) | \\ 384 e_{1u} &\equiv \text{e1t} = r_a |\lambda'(i + 1/2) \; \cos\varphi(j ) | 385 &e_{2u} &\equiv \text{e2t} = r_a |\varphi'(j ) | \\ 386 e_{1v} &\equiv \text{e1t} = r_a |\lambda'(i ) \; \cos\varphi(j + 1/2) | 387 &e_{2v} &\equiv \text{e2t} = r_a |\varphi'(j + 1/2) | \\ 388 e_{1f} &\equiv \text{e1t} = r_a |\lambda'(i + 1/2) \; \cos\varphi(j + 1/2) | 389 &e_{2f} &\equiv \text{e2t} = r_a |\varphi'(j + 1/2) | 390 \end{align*} 386 391 where the last letter of each computational name indicates the grid point considered and 387 392 $r_a$ is the earth radius (defined in \mdl{phycst} along with all universal constants). 388 393 Note that the horizontal position of and scale factors at $w$-points are exactly equal to those of $t$-points, 389 thus no specific arrays are defined at $w$-points. 394 thus no specific arrays are defined at $w$-points. 390 395 391 396 Note that the definition of the scale factors … … 405 410 \begin{figure}[!t] 406 411 \begin{center} 407 \includegraphics[ width=0.90\textwidth]{Fig_zgr_e3}412 \includegraphics[]{Fig_zgr_e3} 408 413 \caption{ 409 414 \protect\label{fig:zgr_e3} 410 415 Comparison of (a) traditional definitions of grid-point position and grid-size in the vertical, 411 416 and (b) analytically derived grid-point position and scale factors. 412 For both grids here, 413 the same $w$-point depth has been chosen but in (a) the $t$-points are set half way between $w$-points while 414 in (b) they are defined from an analytical function: $z(k)=5\,(k-1/2)^3 - 45\,(k-1/2)^2 + 140\,(k-1/2) - 150$. 417 For both grids here, the same $w$-point depth has been chosen but 418 in (a) the $t$-points are set half way between $w$-points while 419 in (b) they are defined from an analytical function: 420 $z(k) = 5 \, (k - 1/2)^3 - 45 \, (k - 1/2)^2 + 140 \, (k - 1/2) - 150$. 415 421 Note the resulting difference between the value of the grid-size $\Delta_k$ and 416 422 those of the scale factor $e_k$. … … 426 432 \label{subsec:DOM_hgr_msh_choice} 427 433 428 429 434 % ------------------------------------------------------------------------------------------------------------- 430 435 % Grid files … … 434 439 435 440 All the arrays relating to a particular ocean model configuration (grid-point position, scale factors, masks) 436 can be saved in files if \np{nn\_msh} $\not = 0$ (namelist variable in \ngn{namdom}).441 can be saved in files if \np{nn\_msh} $\not = 0$ (namelist variable in \ngn{namdom}). 437 442 This can be particularly useful for plots and off-line diagnostics. 438 443 In some cases, the user may choose to make a local modification of a scale factor in the code. … … 441 446 An example is Gibraltar Strait in the ORCA2 configuration. 442 447 When such modifications are done, 443 the output grid written when \np{nn\_msh} $\not = 0$ is no more equal to the input grid.448 the output grid written when \np{nn\_msh} $\not = 0$ is no more equal to the input grid. 444 449 445 450 % ================================================================ … … 466 471 \begin{figure}[!tb] 467 472 \begin{center} 468 \includegraphics[ width=1.0\textwidth]{Fig_z_zps_s_sps}473 \includegraphics[]{Fig_z_zps_s_sps} 469 474 \caption{ 470 475 \protect\label{fig:z_zps_s_sps} … … 475 480 (d) hybrid $s-z$ coordinate, 476 481 (e) hybrid $s-z$ coordinate with partial step, and 477 (f) same as (e) but in the non-linear free surface (\protect\np{ln\_linssh} \forcode{= .false.}).482 (f) same as (e) but in the non-linear free surface (\protect\np{ln\_linssh}~\forcode{= .false.}). 478 483 Note that the non-linear free surface can be used with any of the 5 coordinates (a) to (e). 479 484 } … … 485 490 must be done once of all at the beginning of an experiment. 486 491 It is not intended as an option which can be enabled or disabled in the middle of an experiment. 487 Three main choices are offered (\autoref{fig:z_zps_s_sps} a to c):488 $z$-coordinate with full step bathymetry (\np{ln\_zco} \forcode{= .true.}),489 $z$-coordinate with partial step bathymetry (\np{ln\_zps} \forcode{= .true.}),490 or generalized, $s$-coordinate (\np{ln\_sco} \forcode{= .true.}).492 Three main choices are offered (\autoref{fig:z_zps_s_sps}): 493 $z$-coordinate with full step bathymetry (\np{ln\_zco}~\forcode{= .true.}), 494 $z$-coordinate with partial step bathymetry (\np{ln\_zps}~\forcode{= .true.}), 495 or generalized, $s$-coordinate (\np{ln\_sco}~\forcode{= .true.}). 491 496 Hybridation of the three main coordinates are available: 492 $s-z$ or $s-zps$ coordinate (\autoref{fig:z_zps_s_sps} and \autoref{fig:z_zps_s_sps} e).497 $s-z$ or $s-zps$ coordinate (\autoref{fig:z_zps_s_sps} and \autoref{fig:z_zps_s_sps}). 493 498 By default a non-linear free surface is used: the coordinate follow the time-variation of the free surface so that 494 the transformation is time dependent: $z(i,j,k,t)$ (\autoref{fig:z_zps_s_sps} f).495 When a linear free surface is assumed (\np{ln\_linssh} \forcode{= .true.}),496 the vertical coordinate are fixed in time, but the seawater can move up and down across the z=0surface497 (in other words, the top of the ocean in not a rigid-lid). 499 the transformation is time dependent: $z(i,j,k,t)$ (\autoref{fig:z_zps_s_sps}). 500 When a linear free surface is assumed (\np{ln\_linssh}~\forcode{= .true.}), 501 the vertical coordinate are fixed in time, but the seawater can move up and down across the $z_0$ surface 502 (in other words, the top of the ocean in not a rigid-lid). 498 503 The last choice in terms of vertical coordinate concerns the presence (or not) in 499 504 the model domain of ocean cavities beneath ice shelves. … … 502 507 and partial step are also applied at the ocean/ice shelf interface. 503 508 504 Contrary to the horizontal grid, the vertical grid is computed in the code and 505 no provision is made forreading it from a file.509 Contrary to the horizontal grid, the vertical grid is computed in the code and no provision is made for 510 reading it from a file. 506 511 The only input file is the bathymetry (in meters) (\ifile{bathy\_meter}) 507 512 \footnote{ 508 513 N.B. in full step $z$-coordinate, a \ifile{bathy\_level} file can replace the \ifile{bathy\_meter} file, 509 so that the computation of the number of wet ocean point in each water column is by-passed 510 }. 511 If \np{ln\_isfcav}\forcode{ = .true.}, 512 an extra file input file describing the ice shelf draft (in meters) (\ifile{isf\_draft\_meter}) is needed. 514 so that the computation of the number of wet ocean point in each water column is by-passed}. 515 If \np{ln\_isfcav}~\forcode{= .true.}, an extra file input file (\ifile{isf\_draft\_meter}) describing 516 the ice shelf draft (in meters) is needed. 513 517 514 518 After reading the bathymetry, the algorithm for vertical grid definition differs between the different options: 515 519 \begin{description} 516 520 \item[\textit{zco}] 517 set a reference coordinate transformation $z_0 (k)$, and set $z(i,j,k,t)=z_0(k)$.521 set a reference coordinate transformation $z_0(k)$, and set $z(i,j,k,t) = z_0(k)$. 518 522 \item[\textit{zps}] 519 set a reference coordinate transformation $z_0 (k)$, 520 and calculate the thickness of the deepest level at each $(i,j)$ point using the bathymetry, 521 to obtain the final three-dimensional depth and scale factor arrays. 523 set a reference coordinate transformation $z_0(k)$, and calculate the thickness of the deepest level at 524 each $(i,j)$ point using the bathymetry, to obtain the final three-dimensional depth and scale factor arrays. 522 525 \item[\textit{sco}] 523 smooth the bathymetry to fulfil the hydrostatic consistency criteria and526 smooth the bathymetry to fulfill the hydrostatic consistency criteria and 524 527 set the three-dimensional transformation. 525 528 \item[\textit{s-z} and \textit{s-zps}] 526 smooth the bathymetry to fulfil the hydrostatic consistency criteria and529 smooth the bathymetry to fulfill the hydrostatic consistency criteria and 527 530 set the three-dimensional transformation $z(i,j,k)$, 528 531 and possibly introduce masking of extra land points to better fit the original bathymetry file. … … 532 535 %%% 533 536 534 Unless a linear free surface is used (\np{ln\_linssh} \forcode{= .false.}),537 Unless a linear free surface is used (\np{ln\_linssh}~\forcode{= .false.}), 535 538 the arrays describing the grid point depths and vertical scale factors are three set of 536 539 three dimensional arrays $(i,j,k)$ defined at \textit{before}, \textit{now} and \textit{after} time step. 537 The time at which they are defined is indicated by a suffix: $\_b$, $\_n$, or $\_a$, respectively.540 The time at which they are defined is indicated by a suffix: $\_b$, $\_n$, or $\_a$, respectively. 538 541 They are updated at each model time step using a fixed reference coordinate system which 539 542 computer names have a $\_0$ suffix. 540 When the linear free surface option is used (\np{ln\_linssh}\forcode{ = .true.}), 541 \textit{before}, \textit{now} and \textit{after} arrays are simply set one for all to their reference counterpart. 542 543 When the linear free surface option is used (\np{ln\_linssh}~\forcode{= .true.}), \textit{before}, 544 \textit{now} and \textit{after} arrays are simply set one for all to their reference counterpart. 543 545 544 546 % ------------------------------------------------------------------------------------------------------------- … … 551 553 (found in \ngn{namdom} namelist): 552 554 \begin{description} 553 \item[\np{nn\_bathy} \forcode{= 0}]:555 \item[\np{nn\_bathy}~\forcode{= 0}]: 554 556 a flat-bottom domain is defined. 555 557 The total depth $z_w (jpk)$ is given by the coordinate transformation. 556 The domain can either be a closed basin or a periodic channel depending on the parameter \np{jperio}. 557 \item[\np{nn\_bathy} \forcode{= -1}]:558 The domain can either be a closed basin or a periodic channel depending on the parameter \np{jperio}. 559 \item[\np{nn\_bathy}~\forcode{= -1}]: 558 560 a domain with a bump of topography one third of the domain width at the central latitude. 559 This is meant for the "EEL-R5" configuration, a periodic or open boundary channel with a seamount. 560 \item[\np{nn\_bathy} \forcode{= 1}]:561 This is meant for the "EEL-R5" configuration, a periodic or open boundary channel with a seamount. 562 \item[\np{nn\_bathy}~\forcode{= 1}]: 561 563 read a bathymetry and ice shelf draft (if needed). 562 564 The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters) at … … 569 571 The \ifile{isfdraft\_meter} file (Netcdf format) provides the ice shelf draft (positive, in meters) at 570 572 each grid point of the model grid. 571 This file is only needed if \np{ln\_isfcav} \forcode{= .true.}.573 This file is only needed if \np{ln\_isfcav}~\forcode{= .true.}. 572 574 Defining the ice shelf draft will also define the ice shelf edge and the grounding line position. 573 575 \end{description} 574 576 575 577 When a global ocean is coupled to an atmospheric model it is better to represent all large water bodies 576 ( e.g, great lakes, Caspian sea...)577 even if the model resolution does not allow their communication withthe rest of the ocean.578 (\eg great lakes, Caspian sea...) even if the model resolution does not allow their communication with 579 the rest of the ocean. 578 580 This is unnecessary when the ocean is forced by fixed atmospheric conditions, 579 581 so these seas can be removed from the ocean domain. 580 582 The user has the option to set the bathymetry in closed seas to zero (see \autoref{sec:MISC_closea}), 581 but the code has to be adapted to the user's configuration. 583 but the code has to be adapted to the user's configuration. 582 584 583 585 % ------------------------------------------------------------------------------------------------------------- 584 586 % z-coordinate and reference coordinate transformation 585 587 % ------------------------------------------------------------------------------------------------------------- 586 \subsection[$Z$-coordinate (\protect\np{ln\_zco} \forcode{= .true.}) and ref. coordinate]587 {$Z$-coordinate (\protect\np{ln\_zco} \forcode{= .true.}) and reference coordinate}588 \subsection[$Z$-coordinate (\protect\np{ln\_zco}~\forcode{= .true.}) and ref. coordinate] 589 {$Z$-coordinate (\protect\np{ln\_zco}~\forcode{= .true.}) and reference coordinate} 588 590 \label{subsec:DOM_zco} 589 591 … … 591 593 \begin{figure}[!tb] 592 594 \begin{center} 593 \includegraphics[ width=0.90\textwidth]{Fig_zgr}595 \includegraphics[]{Fig_zgr} 594 596 \caption{ 595 597 \protect\label{fig:zgr} … … 602 604 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 603 605 604 The reference coordinate transformation $z_0 (k)$ defines the arrays $gdept_0$ and $gdepw_0$ for 605 $t$- and $w$-points, respectively. 606 As indicated on \autoref{fig:index_vert} \jp{jpk} is the number of $w$-levels. $gdepw_0(1)$ is the ocean surface. 606 The reference coordinate transformation $z_0(k)$ defines the arrays $gdept_0$ and $gdepw_0$ for $t$- and $w$-points, 607 respectively. 608 As indicated on \autoref{fig:index_vert} \jp{jpk} is the number of $w$-levels. 609 $gdepw_0(1)$ is the ocean surface. 607 610 There are at most \jp{jpk}-1 $t$-points inside the ocean, 608 the additional $t$-point at $jk =jpk$ is below the sea floor and is not used.611 the additional $t$-point at $jk = jpk$ is below the sea floor and is not used. 609 612 The vertical location of $w$- and $t$-levels is defined from the analytic expression of the depth $z_0(k)$ whose 610 613 analytical derivative with respect to $k$ provides the vertical scale factors. … … 613 616 using parameters provided in the \ngn{namcfg} namelist. 614 617 615 It is possible to define a simple regular vertical grid by giving zero stretching (\np{ppacr =0}).616 In that case, 617 the parameters \jp{jpk} (number of $w$-levels) and \np{pphmax} (total ocean depth in meters) fully define the grid. 618 It is possible to define a simple regular vertical grid by giving zero stretching (\np{ppacr}~\forcode{= 0}). 619 In that case, the parameters \jp{jpk} (number of $w$-levels) and 620 \np{pphmax} (total ocean depth in meters) fully define the grid. 618 621 619 622 For climate-related studies it is often desirable to concentrate the vertical resolution near the ocean surface. 620 623 The following function is proposed as a standard for a $z$-coordinate (with either full or partial steps): 621 \begin{ equation}624 \begin{gather} 622 625 \label{eq:DOM_zgr_ana_1} 623 \begin{split} 624 z_0 (k) &= h_{sur} -h_0 \;k-\;h_1 \;\log \left[ {\,\cosh \left( {{(k-h_{th} )} / {h_{cr} }} \right)\,} \right] \\ 625 e_3^0 (k) &= \left| -h_0 -h_1 \;\tanh \left( {{(k-h_{th} )} / {h_{cr} }} \right) \right| 626 \end{split} 627 \end{equation} 628 where $k=1$ to \jp{jpk} for $w$-levels and $k=1$ to $k=1$ for $T-$levels. 626 z_0 (k) = h_{sur} - h_0 \; k - \; h_1 \; \log \big[ \cosh ((k - h_{th}) / h_{cr}) \big] \\ 627 e_3^0(k) = \lt| - h_0 - h_1 \; \tanh \big[ (k - h_{th}) / h_{cr} \big] \rt| 628 \end{gather} 629 where $k = 1$ to \jp{jpk} for $w$-levels and $k = 1$ to $k = 1$ for $T-$levels. 629 630 Such an expression allows us to define a nearly uniform vertical location of levels at the ocean top and bottom with 630 631 a smooth hyperbolic tangent transition in between (\autoref{fig:zgr}). 631 632 632 If the ice shelf cavities are opened (\np{ln\_isfcav} \forcode{= .true.}), the definition of $z_0$ is the same.633 If the ice shelf cavities are opened (\np{ln\_isfcav}~\forcode{= .true.}), the definition of $z_0$ is the same. 633 634 However, definition of $e_3^0$ at $t$- and $w$-points is respectively changed to: 634 635 \begin{equation} 635 636 \label{eq:DOM_zgr_ana_2} 636 637 \begin{split} 637 e_3^T(k) &= z_W (k +1) - z_W (k)\\638 e_3^W(k) &= z_T (k ) - z_T (k-1) \\638 e_3^T(k) &= z_W (k + 1) - z_W (k ) \\ 639 e_3^W(k) &= z_T (k ) - z_T (k - 1) 639 640 \end{split} 640 641 \end{equation} 641 642 This formulation decrease the self-generated circulation into the ice shelf cavity 642 643 (which can, in extreme case, leads to blow up).\\ 643 644 644 645 The most used vertical grid for ORCA2 has $10~m$ ($500~m )$resolution in the surface (bottom) layers and645 The most used vertical grid for ORCA2 has $10~m$ ($500~m$) resolution in the surface (bottom) layers and 646 646 a depth which varies from 0 at the sea surface to a minimum of $-5000~m$. 647 647 This leads to the following conditions: 648 648 \begin{equation} 649 649 \label{eq:DOM_zgr_coef} 650 \begin{split} 651 e_3 (1+1/2) &=10. \\ 652 e_3 (jpk-1/2) &=500. \\ 653 z(1) &=0. \\ 654 z(jpk) &=-5000. \\ 655 \end{split} 650 \begin{array}{ll} 651 e_3 (1 + 1/2) = 10. & z(1 ) = 0. \\ 652 e_3 (jpk - 1/2) = 500. & z(jpk) = -5000. 653 \end{array} 656 654 \end{equation} 657 655 658 With the choice of the stretching $h_{cr} = 3$ and the number of levels \jp{jpk}=$31$,659 the four coefficients $h_{sur}$, $h_ {0}$, $h_{1}$, and $h_{th}$ in656 With the choice of the stretching $h_{cr} = 3$ and the number of levels \jp{jpk}~$= 31$, 657 the four coefficients $h_{sur}$, $h_0$, $h_1$, and $h_{th}$ in 660 658 \autoref{eq:DOM_zgr_ana_2} have been determined such that 661 659 \autoref{eq:DOM_zgr_coef} is satisfied, through an optimisation procedure using a bisection method. 662 660 For the first standard ORCA2 vertical grid this led to the following values: 663 $h_{sur} = 4762.96$, $h_0 =255.58, h_1 =245.5813$, and $h_{th} =21.43336$.661 $h_{sur} = 4762.96$, $h_0 = 255.58, h_1 = 245.5813$, and $h_{th} = 21.43336$. 664 662 The resulting depths and scale factors as a function of the model levels are shown in 665 663 \autoref{fig:zgr} and given in \autoref{tab:orca_zgr}. 666 Those values correspond to the parameters \np{ppsur}, \np{ppa0}, \np{ppa1}, \np{ppkth} in \ngn{namcfg} namelist. 667 668 Rather than entering parameters $h_{sur}$, $h_ {0}$, and $h_{1}$ directly, it is possible to recalculate them.669 In that case the user sets \np{ppsur} \forcode{ = }\np{ppa0}\forcode{ = }\np{ppa1}\forcode{ = 999999}.,664 Those values correspond to the parameters \np{ppsur}, \np{ppa0}, \np{ppa1}, \np{ppkth} in \ngn{namcfg} namelist. 665 666 Rather than entering parameters $h_{sur}$, $h_0$, and $h_1$ directly, it is possible to recalculate them. 667 In that case the user sets \np{ppsur}~$=$~\np{ppa0}~$=$~\np{ppa1}~$= 999999$., 670 668 in \ngn{namcfg} namelist, and specifies instead the four following parameters: 671 669 \begin{itemize} 672 670 \item 673 \np{ppacr} =$h_{cr}$: stretching factor (nondimensional).671 \np{ppacr}~$= h_{cr}$: stretching factor (nondimensional). 674 672 The larger \np{ppacr}, the smaller the stretching. 675 673 Values from $3$ to $10$ are usual. 676 674 \item 677 \np{ppkth} =$h_{th}$: is approximately the model level at which maximum stretching occurs675 \np{ppkth}~$= h_{th}$: is approximately the model level at which maximum stretching occurs 678 676 (nondimensional, usually of order 1/2 or 2/3 of \jp{jpk}) 679 677 \item … … 683 681 \end{itemize} 684 682 As an example, for the $45$ layers used in the DRAKKAR configuration those parameters are: 685 \jp{jpk}\forcode{ = 46}, \np{ppacr}\forcode{ = 9}, \np{ppkth}\forcode{ = 23.563}, 686 \np{ppdzmin}\forcode{ = 6}m, \np{pphmax}\forcode{ = 5750}m. 683 \jp{jpk}~$= 46$, \np{ppacr}~$= 9$, \np{ppkth}~$= 23.563$, \np{ppdzmin}~$= 6~m$, \np{pphmax}~$= 5750~m$. 687 684 688 685 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> … … 691 688 \begin{tabular}{c||r|r|r|r} 692 689 \hline 693 \textbf{LEVEL}& \textbf{gdept\_1d}& \textbf{gdepw\_1d}& \textbf{e3t\_1d }& \textbf{e3w\_1d } \\ \hline 694 1 & \textbf{ 5.00} & 0.00 & \textbf{ 10.00} & 10.00 \\ \hline 695 2 & \textbf{15.00} & 10.00 & \textbf{ 10.00} & 10.00 \\ \hline 696 3 & \textbf{25.00} & 20.00 & \textbf{ 10.00} & 10.00 \\ \hline 697 4 & \textbf{35.01} & 30.00 & \textbf{ 10.01} & 10.00 \\ \hline 698 5 & \textbf{45.01} & 40.01 & \textbf{ 10.01} & 10.01 \\ \hline 699 6 & \textbf{55.03} & 50.02 & \textbf{ 10.02} & 10.02 \\ \hline 700 7 & \textbf{65.06} & 60.04 & \textbf{ 10.04} & 10.03 \\ \hline 701 8 & \textbf{75.13} & 70.09 & \textbf{ 10.09} & 10.06 \\ \hline 702 9 & \textbf{85.25} & 80.18 & \textbf{ 10.17} & 10.12 \\ \hline 703 10 & \textbf{95.49} & 90.35 & \textbf{ 10.33} & 10.24 \\ \hline 704 11 & \textbf{105.97} & 100.69 & \textbf{ 10.65} & 10.47 \\ \hline 705 12 & \textbf{116.90} & 111.36 & \textbf{ 11.27} & 10.91 \\ \hline 706 13 & \textbf{128.70} & 122.65 & \textbf{ 12.47} & 11.77 \\ \hline 707 14 & \textbf{142.20} & 135.16 & \textbf{ 14.78} & 13.43 \\ \hline 708 15 & \textbf{158.96} & 150.03 & \textbf{ 19.23} & 16.65 \\ \hline 709 16 & \textbf{181.96} & 169.42 & \textbf{ 27.66} & 22.78 \\ \hline 710 17 & \textbf{216.65} & 197.37 & \textbf{ 43.26} & 34.30 \\ \hline 711 18 & \textbf{272.48} & 241.13 & \textbf{ 70.88} & 55.21 \\ \hline 712 19 & \textbf{364.30} & 312.74 & \textbf{116.11} & 90.99 \\ \hline 713 20 & \textbf{511.53} & 429.72 & \textbf{181.55} & 146.43 \\ \hline 714 21 & \textbf{732.20} & 611.89 & \textbf{261.03} & 220.35 \\ \hline 715 22 & \textbf{1033.22}& 872.87 & \textbf{339.39} & 301.42 \\ \hline 716 23 & \textbf{1405.70}& 1211.59 & \textbf{402.26} & 373.31 \\ \hline 717 24 & \textbf{1830.89}& 1612.98 & \textbf{444.87} & 426.00 \\ \hline 718 25 & \textbf{2289.77}& 2057.13 & \textbf{470.55} & 459.47 \\ \hline 719 26 & \textbf{2768.24}& 2527.22 & \textbf{484.95} & 478.83 \\ \hline 720 27 & \textbf{3257.48}& 3011.90 & \textbf{492.70} & 489.44 \\ \hline 721 28 & \textbf{3752.44}& 3504.46 & \textbf{496.78} & 495.07 \\ \hline 722 29 & \textbf{4250.40}& 4001.16 & \textbf{498.90} & 498.02 \\ \hline 723 30 & \textbf{4749.91}& 4500.02 & \textbf{500.00} & 499.54 \\ \hline 724 31 & \textbf{5250.23}& 5000.00 & \textbf{500.56} & 500.33 \\ \hline 690 \textbf{LEVEL} & \textbf{gdept\_1d} & \textbf{gdepw\_1d} & \textbf{e3t\_1d } & \textbf{e3w\_1d} \\ 691 \hline 692 1 & \textbf{ 5.00} & 0.00 & \textbf{ 10.00} & 10.00 \\ 693 \hline 694 2 & \textbf{ 15.00} & 10.00 & \textbf{ 10.00} & 10.00 \\ 695 \hline 696 3 & \textbf{ 25.00} & 20.00 & \textbf{ 10.00} & 10.00 \\ 697 \hline 698 4 & \textbf{ 35.01} & 30.00 & \textbf{ 10.01} & 10.00 \\ 699 \hline 700 5 & \textbf{ 45.01} & 40.01 & \textbf{ 10.01} & 10.01 \\ 701 \hline 702 6 & \textbf{ 55.03} & 50.02 & \textbf{ 10.02} & 10.02 \\ 703 \hline 704 7 & \textbf{ 65.06} & 60.04 & \textbf{ 10.04} & 10.03 \\ 705 \hline 706 8 & \textbf{ 75.13} & 70.09 & \textbf{ 10.09} & 10.06 \\ 707 \hline 708 9 & \textbf{ 85.25} & 80.18 & \textbf{ 10.17} & 10.12 \\ 709 \hline 710 10 & \textbf{ 95.49} & 90.35 & \textbf{ 10.33} & 10.24 \\ 711 \hline 712 11 & \textbf{ 105.97} & 100.69 & \textbf{ 10.65} & 10.47 \\ 713 \hline 714 12 & \textbf{ 116.90} & 111.36 & \textbf{ 11.27} & 10.91 \\ 715 \hline 716 13 & \textbf{ 128.70} & 122.65 & \textbf{ 12.47} & 11.77 \\ 717 \hline 718 14 & \textbf{ 142.20} & 135.16 & \textbf{ 14.78} & 13.43 \\ 719 \hline 720 15 & \textbf{ 158.96} & 150.03 & \textbf{ 19.23} & 16.65 \\ 721 \hline 722 16 & \textbf{ 181.96} & 169.42 & \textbf{ 27.66} & 22.78 \\ 723 \hline 724 17 & \textbf{ 216.65} & 197.37 & \textbf{ 43.26} & 34.30 \\ 725 \hline 726 18 & \textbf{ 272.48} & 241.13 & \textbf{ 70.88} & 55.21 \\ 727 \hline 728 19 & \textbf{ 364.30} & 312.74 & \textbf{ 116.11} & 90.99 \\ 729 \hline 730 20 & \textbf{ 511.53} & 429.72 & \textbf{ 181.55} & 146.43 \\ 731 \hline 732 21 & \textbf{ 732.20} & 611.89 & \textbf{ 261.03} & 220.35 \\ 733 \hline 734 22 & \textbf{ 1033.22} & 872.87 & \textbf{ 339.39} & 301.42 \\ 735 \hline 736 23 & \textbf{ 1405.70} & 1211.59 & \textbf{ 402.26} & 373.31 \\ 737 \hline 738 24 & \textbf{ 1830.89} & 1612.98 & \textbf{ 444.87} & 426.00 \\ 739 \hline 740 25 & \textbf{ 2289.77} & 2057.13 & \textbf{ 470.55} & 459.47 \\ 741 \hline 742 26 & \textbf{ 2768.24} & 2527.22 & \textbf{ 484.95} & 478.83 \\ 743 \hline 744 27 & \textbf{ 3257.48} & 3011.90 & \textbf{ 492.70} & 489.44 \\ 745 \hline 746 28 & \textbf{ 3752.44} & 3504.46 & \textbf{ 496.78} & 495.07 \\ 747 \hline 748 29 & \textbf{ 4250.40} & 4001.16 & \textbf{ 498.90} & 498.02 \\ 749 \hline 750 30 & \textbf{ 4749.91} & 4500.02 & \textbf{ 500.00} & 499.54 \\ 751 \hline 752 31 & \textbf{ 5250.23} & 5000.00 & \textbf{ 500.56} & 500.33 \\ 753 \hline 725 754 \end{tabular} 726 755 \end{center} … … 736 765 % z-coordinate with partial step 737 766 % ------------------------------------------------------------------------------------------------------------- 738 \subsection{$Z$-coordinate with partial step (\protect\np{ln\_zps} \forcode{= .true.})}767 \subsection{$Z$-coordinate with partial step (\protect\np{ln\_zps}~\forcode{= .true.})} 739 768 \label{subsec:DOM_zps} 740 769 %--------------------------------------------namdom------------------------------------------------------- … … 744 773 745 774 In $z$-coordinate partial step, 746 the depths of the model levels are defined by the reference analytical function $z_0 747 the previous section, \ emph{except} in the bottom layer.775 the depths of the model levels are defined by the reference analytical function $z_0(k)$ as described in 776 the previous section, \textit{except} in the bottom layer. 748 777 The thickness of the bottom layer is allowed to vary as a function of geographical location $(\lambda,\varphi)$ to 749 778 allow a better representation of the bathymetry, especially in the case of small slopes … … 752 781 With partial steps, layers from 1 to \jp{jpk}-2 can have a thickness smaller than $e_{3t}(jk)$. 753 782 The model deepest layer (\jp{jpk}-1) is allowed to have either a smaller or larger thickness than $e_{3t}(jpk)$: 754 the maximum thickness allowed is $2*e_{3t}(jpk -1)$.783 the maximum thickness allowed is $2*e_{3t}(jpk - 1)$. 755 784 This has to be kept in mind when specifying values in \ngn{namdom} namelist, 756 785 as the maximum depth \np{pphmax} in partial steps: 757 for example, with \np{pphmax} $=5750~m$ for the DRAKKAR 45 layer grid,758 the maximum ocean depth allowed is actually $6000~m$ (the default thickness $e_{3t}(jpk -1)$ being $250~m$).786 for example, with \np{pphmax}~$= 5750~m$ for the DRAKKAR 45 layer grid, 787 the maximum ocean depth allowed is actually $6000~m$ (the default thickness $e_{3t}(jpk - 1)$ being $250~m$). 759 788 Two variables in the namdom namelist are used to define the partial step vertical grid. 760 789 The mimimum water thickness (in meters) allowed for a cell partially filled with bathymetry at level jk is … … 767 796 % s-coordinate 768 797 % ------------------------------------------------------------------------------------------------------------- 769 \subsection{$S$-coordinate (\protect\np{ln\_sco} \forcode{= .true.})}798 \subsection{$S$-coordinate (\protect\np{ln\_sco}~\forcode{= .true.})} 770 799 \label{subsec:DOM_sco} 771 800 %------------------------------------------nam_zgr_sco--------------------------------------------------- … … 774 803 %-------------------------------------------------------------------------------------------------------------- 775 804 Options are defined in \ngn{namzgr\_sco}. 776 In $s$-coordinate (\np{ln\_sco} \forcode{= .true.}), the depth and thickness of the model levels are defined from805 In $s$-coordinate (\np{ln\_sco}~\forcode{= .true.}), the depth and thickness of the model levels are defined from 777 806 the product of a depth field and either a stretching function or its derivative, respectively: 778 807 779 \ [808 \begin{align*} 780 809 % \label{eq:DOM_sco_ana} 781 \begin{split} 782 z(k) &= h(i,j) \; z_0(k) \\ 783 e_3(k) &= h(i,j) \; z_0'(k) 784 \end{split} 785 \] 810 z(k) &= h(i,j) \; z_0 (k) \\ 811 e_3(k) &= h(i,j) \; z_0'(k) 812 \end{align*} 786 813 787 814 where $h$ is the depth of the last $w$-level ($z_0(k)$) defined at the $t$-point location in the horizontal and … … 789 816 The depth field $h$ is not necessary the ocean depth, 790 817 since a mixed step-like and bottom-following representation of the topography can be used 791 (\autoref{fig:z_zps_s_sps} d-e) or an envelop bathymetry can be defined (\autoref{fig:z_zps_s_sps}f).818 (\autoref{fig:z_zps_s_sps}) or an envelop bathymetry can be defined (\autoref{fig:z_zps_s_sps}). 792 819 The namelist parameter \np{rn\_rmax} determines the slope at which 793 the terrain-following coordinate intersects the sea bed and becomes a pseudo z-coordinate. 820 the terrain-following coordinate intersects the sea bed and becomes a pseudo z-coordinate. 794 821 The coordinate can also be hybridised by specifying \np{rn\_sbot\_min} and \np{rn\_sbot\_max} as 795 822 the minimum and maximum depths at which the terrain-following vertical coordinate is calculated. … … 799 826 800 827 The original default NEMO s-coordinate stretching is available if neither of the other options are specified as true 801 (\np{ln\_s\_SH94} \forcode{ = .false.} and \np{ln\_s\_SF12}\forcode{ = .false.}).828 (\np{ln\_s\_SH94}~\forcode{= .false.} and \np{ln\_s\_SF12}~\forcode{= .false.}). 802 829 This uses a depth independent $\tanh$ function for the stretching \citep{Madec_al_JPO96}: 803 830 804 831 \[ 805 z = s_{min} +C\left(s\right)\left(H-s_{min}\right)832 z = s_{min} + C (s) (H - s_{min}) 806 833 % \label{eq:SH94_1} 807 834 \] … … 810 837 allows a $z$-coordinate to placed on top of the stretched coordinate, 811 838 and $z$ is the depth (negative down from the asea surface). 839 \begin{gather*} 840 s = - \frac{k}{n - 1} \quad \text{and} \quad 0 \leq k \leq n - 1 841 % \label{eq:DOM_s} 842 \\ 843 % \label{eq:DOM_sco_function} 844 C(s) = \frac{[\tanh(\theta \, (s + b)) - \tanh(\theta \, b)]}{2 \; \sinh(\theta)} 845 \end{gather*} 846 847 A stretching function, 848 modified from the commonly used \citet{Song_Haidvogel_JCP94} stretching (\np{ln\_s\_SH94}~\forcode{= .true.}), 849 is also available and is more commonly used for shelf seas modelling: 812 850 813 851 \[ 814 s = -\frac{k}{n-1} \quad \text{ and } \quad 0 \leq k \leq n-1 815 % \label{eq:DOM_s} 816 \] 817 818 \[ 819 % \label{eq:DOM_sco_function} 820 \begin{split} 821 C(s) &= \frac{ \left[ \tanh{ \left( \theta \, (s+b) \right)} 822 - \tanh{ \left( \theta \, b \right)} \right]} 823 {2\;\sinh \left( \theta \right)} 824 \end{split} 825 \] 826 827 A stretching function, 828 modified from the commonly used \citet{Song_Haidvogel_JCP94} stretching (\np{ln\_s\_SH94}\forcode{ = .true.}), 829 is also available and is more commonly used for shelf seas modelling: 830 831 \[ 832 C\left(s\right) = \left(1 - b \right)\frac{ \sinh\left( \theta s\right)}{\sinh\left(\theta\right)} + \\ 833 b\frac{ \tanh \left[ \theta \left(s + \frac{1}{2} \right)\right] - \tanh\left(\frac{\theta}{2}\right)}{ 2\tanh\left (\frac{\theta}{2}\right)} 852 C(s) = (1 - b) \frac{\sinh(\theta s)}{\sinh(\theta)} 853 + b \frac{\tanh \lt[ \theta \lt(s + \frac{1}{2} \rt) \rt] - \tanh \lt( \frac{\theta}{2} \rt)} 854 { 2 \tanh \lt( \frac{\theta}{2} \rt)} 834 855 % \label{eq:SH94_2} 835 856 \] … … 838 859 \begin{figure}[!ht] 839 860 \begin{center} 840 \includegraphics[ width=1.0\textwidth]{Fig_sco_function}861 \includegraphics[]{Fig_sco_function} 841 862 \caption{ 842 863 \protect\label{fig:sco_function} … … 848 869 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 849 870 850 where $H_c$ is the critical depth (\np{rn\_hc}) at which 851 the coordinate transitions from pure $\sigma$ to the stretched coordinate, 852 and $\theta$ (\np{rn\_theta}) and $b$ (\np{rn\_bb}) are the surface and bottom control parameters such that 853 $0\leqslant \theta \leqslant 20$, and $0\leqslant b\leqslant 1$. 871 where $H_c$ is the critical depth (\np{rn\_hc}) at which the coordinate transitions from pure $\sigma$ to 872 the stretched coordinate, and $\theta$ (\np{rn\_theta}) and $b$ (\np{rn\_bb}) are the surface and 873 bottom control parameters such that $0 \leqslant \theta \leqslant 20$, and $0 \leqslant b \leqslant 1$. 854 874 $b$ has been designed to allow surface and/or bottom increase of the vertical resolution 855 875 (\autoref{fig:sco_function}). … … 859 879 In this case the a stretching function $\gamma$ is defined such that: 860 880 861 \ [862 z = - \gamma h \quad \text{ with} \quad 0 \leq \gamma \leq 1881 \begin{equation} 882 z = - \gamma h \quad \text{with} \quad 0 \leq \gamma \leq 1 863 883 % \label{eq:z} 864 \ ]884 \end{equation} 865 885 866 886 The function is defined with respect to $\sigma$, the unstretched terrain-following coordinate: 867 887 868 \ [888 \begin{gather*} 869 889 % \label{eq:DOM_gamma_deriv} 870 \gamma= A\left(\sigma-\frac{1}{2}\left(\sigma^{2}+f\left(\sigma\right)\right)\right)+B\left(\sigma^{3}-f\left(\sigma\right)\right)+f\left(\sigma\right) 871 \] 872 873 Where: 874 \[ 890 \gamma = A \lt( \sigma - \frac{1}{2} (\sigma^2 + f (\sigma)) \rt) 891 + B \lt( \sigma^3 - f (\sigma) \rt) + f (\sigma) \\ 892 \intertext{Where:} 875 893 % \label{eq:DOM_gamma} 876 f\left(\sigma\right)=\left(\alpha+2\right)\sigma^{\alpha+1}-\left(\alpha+1\right)\sigma^{\alpha+2} \quad \text{ and } \quad \sigma = \frac{k}{n-1} 877 \] 894 f(\sigma) = (\alpha + 2) \sigma^{\alpha + 1} - (\alpha + 1) \sigma^{\alpha + 2} 895 \quad \text{and} \quad \sigma = \frac{k}{n - 1} 896 \end{gather*} 878 897 879 898 This gives an analytical stretching of $\sigma$ that is solvable in $A$ and $B$ as a function of … … 892 911 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 893 912 \begin{figure}[!ht] 894 \includegraphics[width=1.0\textwidth]{Fig_DOM_compare_coordinates_surface}895 896 897 898 the \citet{Siddorn_Furner_OM12} $S$-coordinate (dashed lines) in899 the surface 100m for a idealised bathymetry that goes from 50m to 5500mdepth.900 901 902 913 \includegraphics[]{Fig_DOM_compare_coordinates_surface} 914 \caption{ 915 A comparison of the \citet{Song_Haidvogel_JCP94} $S$-coordinate (solid lines), 916 a 50 level $Z$-coordinate (contoured surfaces) and 917 the \citet{Siddorn_Furner_OM12} $S$-coordinate (dashed lines) in the surface $100~m$ for 918 a idealised bathymetry that goes from $50~m$ to $5500~m$ depth. 919 For clarity every third coordinate surface is shown. 920 } 921 \label{fig:fig_compare_coordinates_surface} 903 922 \end{figure} 904 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>923 % >>>>>>>>>>>>>>>>>>>>>>>>>>>> 905 924 906 925 This gives a smooth analytical stretching in computational space that is constrained to … … 925 944 926 945 % ------------------------------------------------------------------------------------------------------------- 927 % \zstar- or \sstar-coordinate928 % ------------------------------------------------------------------------------------------------------------- 929 \subsection{ $Z^*$- or $S^*$-coordinate (\protect\np{ln\_linssh}\forcode{ = .false.})}946 % z*- or s*-coordinate 947 % ------------------------------------------------------------------------------------------------------------- 948 \subsection{\zstar- or \sstar-coordinate (\protect\np{ln\_linssh}~\forcode{= .false.})} 930 949 \label{subsec:DOM_zgr_star} 931 950 932 This option is described in the Report by Levier \textit{et al.} (2007), available on the \NEMO web site. 951 This option is described in the Report by Levier \textit{et al.} (2007), available on the \NEMO web site. 933 952 934 953 %gm% key advantage: minimise the diffusion/dispertion associated with advection in response to high frequency surface disturbances … … 940 959 \label{subsec:DOM_msk} 941 960 942 Whatever the vertical coordinate used, 943 the model offers the possibility of representing the bottom topography with steps that 944 follow the face of the model cells (step like topography) \citep{Madec_al_JPO96}. 945 The distribution of the steps in the horizontal is defined in a 2D integer array, mbathy, 946 which gives the number of ocean levels (\ie those that are not masked) at each $t$-point. 947 mbathy is computed from the meter bathymetry using the definiton of gdept as 948 the number of $t$-points which gdept $\leq$ bathy. 961 Whatever the vertical coordinate used, the model offers the possibility of representing the bottom topography with 962 steps that follow the face of the model cells (step like topography) \citep{Madec_al_JPO96}. 963 The distribution of the steps in the horizontal is defined in a 2D integer array, mbathy, which 964 gives the number of ocean levels (\ie those that are not masked) at each $t$-point. 965 mbathy is computed from the meter bathymetry using the definiton of gdept as the number of $t$-points which 966 gdept $\leq$ bathy. 949 967 950 968 Modifications of the model bathymetry are performed in the \textit{bat\_ctl} routine (see \mdl{domzgr} module) after … … 954 972 As for the representation of bathymetry, a 2D integer array, misfdep, is created. 955 973 misfdep defines the level of the first wet $t$-point. 956 All the cells between $k =1$ and $misfdep(i,j)-1$ are masked.957 By default, misfdep(:,:)=1and no cells are masked.974 All the cells between $k = 1$ and $misfdep(i,j) - 1$ are masked. 975 By default, $misfdep(:,:) = 1$ and no cells are masked. 958 976 959 977 In case of ice shelf cavities, modifications of the model bathymetry and ice shelf draft into 960 978 the cavities are performed in the \textit{zgr\_isf} routine. 961 The compatibility between ice shelf draft and bathymetry is checked. 962 All the locations where the isf cavity is thinnest than \np{rn\_isfhmin} meters are grounded (\ie masked). 979 The compatibility between ice shelf draft and bathymetry is checked. 980 All the locations where the isf cavity is thinnest than \np{rn\_isfhmin} meters are grounded (\ie masked). 963 981 If only one cell on the water column is opened at $t$-, $u$- or $v$-points, 964 982 the bathymetry or the ice shelf draft is dug to fit this constrain. 965 If the incompatibility is too strong (need to dig more than 1 cell), the cell is masked. \\983 If the incompatibility is too strong (need to dig more than 1 cell), the cell is masked. 966 984 967 985 From the \textit{mbathy} and \textit{misfdep} array, the mask fields are defined as follows: 968 \begin{align*} 969 tmask(i,j,k) &= \begin{cases} \; 0& \text{ if $k < misfdep(i,j) $ } \\ 970 \; 1& \text{ if $misfdep(i,j) \leq k\leq mbathy(i,j)$ } \\ 971 \; 0& \text{ if $k > mbathy(i,j)$ } \end{cases} \\ 972 umask(i,j,k) &= \; tmask(i,j,k) \ * \ tmask(i+1,j,k) \\ 973 vmask(i,j,k) &= \; tmask(i,j,k) \ * \ tmask(i,j+1,k) \\ 974 fmask(i,j,k) &= \; tmask(i,j,k) \ * \ tmask(i+1,j,k) \\ 975 & \ \ \, * tmask(i,j,k) \ * \ tmask(i+1,j,k) \\ 976 wmask(i,j,k) &= \; tmask(i,j,k) \ * \ tmask(i,j,k-1) \text{ with } wmask(i,j,1) = tmask(i,j,1) 977 \end{align*} 986 \begin{alignat*}{2} 987 tmask(i,j,k) &= & & 988 \begin{cases} 989 0 &\text{if $ k < misfdep(i,j)$} \\ 990 1 &\text{if $misfdep(i,j) \leq k \leq mbathy(i,j)$} \\ 991 0 &\text{if $ k > mbathy(i,j)$} 992 \end{cases} 993 \\ 994 umask(i,j,k) &= & &tmask(i,j,k) * tmask(i + 1,j, k) \\ 995 vmask(i,j,k) &= & &tmask(i,j,k) * tmask(i ,j + 1,k) \\ 996 fmask(i,j,k) &= & &tmask(i,j,k) * tmask(i + 1,j, k) \\ 997 & &* &tmask(i,j,k) * tmask(i + 1,j, k) \\ 998 wmask(i,j,k) &= & &tmask(i,j,k) * tmask(i ,j,k - 1) \\ 999 \text{with~} wmask(i,j,1) &= & &tmask(i,j,1) 1000 \end{alignat*} 978 1001 979 1002 Note that, without ice shelves cavities, 980 1003 masks at $t-$ and $w-$points are identical with the numerical indexing used (\autoref{subsec:DOM_Num_Index}). 981 1004 Nevertheless, $wmask$ are required with ocean cavities to deal with the top boundary (ice shelf/ocean interface) 982 exactly in the same way as for the bottom boundary. 1005 exactly in the same way as for the bottom boundary. 983 1006 984 1007 The specification of closed lateral boundaries requires that at least 985 1008 the first and last rows and columns of the \textit{mbathy} array are set to zero. 986 In the particular case of an east-west cyclical boundary condition, 987 \textit{mbathy} has its last column equal to the second one and its first column equal to the last but one 988 (and so too the mask arrays) (see \autoref{fig:LBC_jperio}). 989 1009 In the particular case of an east-west cyclical boundary condition, \textit{mbathy} has its last column equal to 1010 the second one and its first column equal to the last but one (and so too the mask arrays) 1011 (see \autoref{fig:LBC_jperio}). 990 1012 991 1013 % ================================================================ … … 1000 1022 1001 1023 Options are defined in \ngn{namtsd}. 1002 By default, the ocean start from rest (the velocity field is set to zero) and the initialization of temperature and salinity fields is controlled through the \np{ln\_tsd\_ini} namelist parameter. 1024 By default, the ocean start from rest (the velocity field is set to zero) and the initialization of temperature and 1025 salinity fields is controlled through the \np{ln\_tsd\_ini} namelist parameter. 1003 1026 \begin{description} 1004 \item[\np{ln\_tsd\_init} \forcode{= .true.}]1027 \item[\np{ln\_tsd\_init}~\forcode{= .true.}] 1005 1028 use a T and S input files that can be given on the model grid itself or on their native input data grid. 1006 1029 In the latter case, … … 1009 1032 The information relative to the input files are given in the \np{sn\_tem} and \np{sn\_sal} structures. 1010 1033 The computation is done in the \mdl{dtatsd} module. 1011 \item[\np{ln\_tsd\_init} \forcode{= .false.}]1012 use constant salinity value of 35.5 psu and an analytical profile of temperature (typical of the tropical ocean),1013 see \rou{istate\_t\_s} subroutine called from \mdl{istate} module.1034 \item[\np{ln\_tsd\_init}~\forcode{= .false.}] 1035 use constant salinity value of $35.5~psu$ and an analytical profile of temperature 1036 (typical of the tropical ocean), see \rou{istate\_t\_s} subroutine called from \mdl{istate} module. 1014 1037 \end{description} 1015 1038
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