1 | \documentclass[../main/NEMO_manual]{subfiles} |
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2 | |
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3 | \begin{document} |
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4 | % ================================================================ |
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5 | % Chapter — Lateral Boundary Condition (LBC) |
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6 | % ================================================================ |
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7 | \chapter{Lateral Boundary Condition (LBC)} |
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8 | \label{chap:LBC} |
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9 | |
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10 | \chaptertoc |
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11 | |
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12 | \newpage |
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13 | |
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14 | %gm% add here introduction to this chapter |
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15 | |
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16 | % ================================================================ |
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17 | % Boundary Condition at the Coast |
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18 | % ================================================================ |
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19 | \section[Boundary condition at the coast (\texttt{rn\_shlat})] |
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20 | {Boundary condition at the coast (\protect\np{rn\_shlat})} |
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21 | \label{sec:LBC_coast} |
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22 | %--------------------------------------------nam_lbc------------------------------------------------------- |
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23 | |
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24 | \nlst{namlbc} |
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25 | %-------------------------------------------------------------------------------------------------------------- |
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26 | |
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27 | %The lateral ocean boundary conditions contiguous to coastlines are Neumann conditions for heat and salt |
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28 | %(no flux across boundaries) and Dirichlet conditions for momentum (ranging from free-slip to "strong" no-slip). |
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29 | %They are handled automatically by the mask system (see \autoref{subsec:DOM_msk}). |
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30 | |
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31 | %OPA allows land and topography grid points in the computational domain due to the presence of continents or islands, |
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32 | %and includes the use of a full or partial step representation of bottom topography. |
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33 | %The computation is performed over the whole domain, \ie\ we do not try to restrict the computation to ocean-only points. |
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34 | %This choice has two motivations. |
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35 | %Firstly, working on ocean only grid points overloads the code and harms the code readability. |
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36 | %Secondly, and more importantly, it drastically reduces the vector portion of the computation, |
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37 | %leading to a dramatic increase of CPU time requirement on vector computers. |
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38 | %The current section describes how the masking affects the computation of the various terms of the equations |
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39 | %with respect to the boundary condition at solid walls. |
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40 | %The process of defining which areas are to be masked is described in \autoref{subsec:DOM_msk}. |
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41 | |
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42 | Options are defined through the \nam{lbc} namelist variables. |
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43 | The discrete representation of a domain with complex boundaries (coastlines and bottom topography) leads to |
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44 | arrays that include large portions where a computation is not required as the model variables remain at zero. |
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45 | Nevertheless, vectorial supercomputers are far more efficient when computing over a whole array, |
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46 | and the readability of a code is greatly improved when boundary conditions are applied in |
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47 | an automatic way rather than by a specific computation before or after each computational loop. |
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48 | An efficient way to work over the whole domain while specifying the boundary conditions, |
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49 | is to use multiplication by mask arrays in the computation. |
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50 | A mask array is a matrix whose elements are $1$ in the ocean domain and $0$ elsewhere. |
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51 | A simple multiplication of a variable by its own mask ensures that it will remain zero over land areas. |
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52 | Since most of the boundary conditions consist of a zero flux across the solid boundaries, |
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53 | they can be simply applied by multiplying variables by the correct mask arrays, |
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54 | \ie\ the mask array of the grid point where the flux is evaluated. |
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55 | For example, the heat flux in the \textbf{i}-direction is evaluated at $u$-points. |
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56 | Evaluating this quantity as, |
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57 | |
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58 | \[ |
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59 | % \label{eq:lbc_aaaa} |
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60 | \frac{A^{lT} }{e_1 }\frac{\partial T}{\partial i}\equiv \frac{A_u^{lT} |
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61 | }{e_{1u} } \; \delta_{i+1 / 2} \left[ T \right]\;\;mask_u |
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62 | \] |
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63 | (where mask$_{u}$ is the mask array at a $u$-point) ensures that the heat flux is zero inside land and |
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64 | at the boundaries, since mask$_{u}$ is zero at solid boundaries which in this case are defined at $u$-points |
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65 | (normal velocity $u$ remains zero at the coast) (\autoref{fig:LBC_uv}). |
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66 | |
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67 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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68 | \begin{figure}[!t] |
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69 | \begin{center} |
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70 | \includegraphics[width=\textwidth]{Fig_LBC_uv} |
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71 | \caption{ |
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72 | \protect\label{fig:LBC_uv} |
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73 | Lateral boundary (thick line) at T-level. |
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74 | The velocity normal to the boundary is set to zero. |
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75 | } |
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76 | \end{center} |
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77 | \end{figure} |
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78 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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79 | |
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80 | For momentum the situation is a bit more complex as two boundary conditions must be provided along the coast |
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81 | (one each for the normal and tangential velocities). |
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82 | The boundary of the ocean in the C-grid is defined by the velocity-faces. |
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83 | For example, at a given $T$-level, |
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84 | the lateral boundary (a coastline or an intersection with the bottom topography) is made of |
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85 | segments joining $f$-points, and normal velocity points are located between two $f-$points (\autoref{fig:LBC_uv}). |
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86 | The boundary condition on the normal velocity (no flux through solid boundaries) |
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87 | can thus be easily implemented using the mask system. |
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88 | The boundary condition on the tangential velocity requires a more specific treatment. |
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89 | This boundary condition influences the relative vorticity and momentum diffusive trends, |
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90 | and is required in order to compute the vorticity at the coast. |
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91 | Four different types of lateral boundary condition are available, |
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92 | controlled by the value of the \np{rn\_shlat} namelist parameter |
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93 | (The value of the mask$_{f}$ array along the coastline is set equal to this parameter). |
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94 | These are: |
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95 | |
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96 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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97 | \begin{figure}[!p] |
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98 | \begin{center} |
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99 | \includegraphics[width=\textwidth]{Fig_LBC_shlat} |
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100 | \caption{ |
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101 | \protect\label{fig:LBC_shlat} |
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102 | lateral boundary condition |
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103 | (a) free-slip ($rn\_shlat=0$); |
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104 | (b) no-slip ($rn\_shlat=2$); |
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105 | (c) "partial" free-slip ($0<rn\_shlat<2$) and |
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106 | (d) "strong" no-slip ($2<rn\_shlat$). |
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107 | Implied "ghost" velocity inside land area is display in grey. |
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108 | } |
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109 | \end{center} |
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110 | \end{figure} |
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111 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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112 | |
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113 | \begin{description} |
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114 | |
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115 | \item[free-slip boundary condition (\np{rn\_shlat}\forcode{ = 0}):] the tangential velocity at |
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116 | the coastline is equal to the offshore velocity, |
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117 | \ie\ the normal derivative of the tangential velocity is zero at the coast, |
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118 | so the vorticity: mask$_{f}$ array is set to zero inside the land and just at the coast |
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119 | (\autoref{fig:LBC_shlat}-a). |
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120 | |
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121 | \item[no-slip boundary condition (\np{rn\_shlat}\forcode{ = 2}):] the tangential velocity vanishes at the coastline. |
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122 | Assuming that the tangential velocity decreases linearly from |
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123 | the closest ocean velocity grid point to the coastline, |
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124 | the normal derivative is evaluated as if the velocities at the closest land velocity gridpoint and |
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125 | the closest ocean velocity gridpoint were of the same magnitude but in the opposite direction |
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126 | (\autoref{fig:LBC_shlat}-b). |
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127 | Therefore, the vorticity along the coastlines is given by: |
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128 | |
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129 | \[ |
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130 | \zeta \equiv 2 \left(\delta_{i+1/2} \left[e_{2v} v \right] - \delta_{j+1/2} \left[e_{1u} u \right] \right) / \left(e_{1f} e_{2f} \right) \ , |
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131 | \] |
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132 | where $u$ and $v$ are masked fields. |
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133 | Setting the mask$_{f}$ array to $2$ along the coastline provides a vorticity field computed with |
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134 | the no-slip boundary condition, simply by multiplying it by the mask$_{f}$ : |
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135 | \[ |
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136 | % \label{eq:lbc_bbbb} |
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137 | \zeta \equiv \frac{1}{e_{1f} {\kern 1pt}e_{2f} }\left( {\delta_{i+1/2} |
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138 | \left[ {e_{2v} \,v} \right]-\delta_{j+1/2} \left[ {e_{1u} \,u} \right]} |
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139 | \right)\;\mbox{mask}_f |
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140 | \] |
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141 | |
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142 | \item["partial" free-slip boundary condition (0$<$\np{rn\_shlat}$<$2):] the tangential velocity at |
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143 | the coastline is smaller than the offshore velocity, \ie\ there is a lateral friction but |
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144 | not strong enough to make the tangential velocity at the coast vanish (\autoref{fig:LBC_shlat}-c). |
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145 | This can be selected by providing a value of mask$_{f}$ strictly inbetween $0$ and $2$. |
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146 | |
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147 | \item["strong" no-slip boundary condition (2$<$\np{rn\_shlat}):] the viscous boundary layer is assumed to |
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148 | be smaller than half the grid size (\autoref{fig:LBC_shlat}-d). |
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149 | The friction is thus larger than in the no-slip case. |
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150 | |
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151 | \end{description} |
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152 | |
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153 | Note that when the bottom topography is entirely represented by the $s$-coordinates (pure $s$-coordinate), |
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154 | the lateral boundary condition on tangential velocity is of much less importance as |
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155 | it is only applied next to the coast where the minimum water depth can be quite shallow. |
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156 | |
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157 | |
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158 | % ================================================================ |
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159 | % Boundary Condition around the Model Domain |
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160 | % ================================================================ |
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161 | \section[Model domain boundary condition (\texttt{jperio})] |
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162 | {Model domain boundary condition (\protect\jp{jperio})} |
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163 | \label{sec:LBC_jperio} |
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164 | |
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165 | At the model domain boundaries several choices are offered: |
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166 | closed, cyclic east-west, cyclic north-south, a north-fold, and combination closed-north fold or |
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167 | bi-cyclic east-west and north-fold. |
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168 | The north-fold boundary condition is associated with the 3-pole ORCA mesh. |
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169 | |
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170 | % ------------------------------------------------------------------------------------------------------------- |
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171 | % Closed, cyclic (\jp{jperio}\forcode{ = 0..2}) |
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172 | % ------------------------------------------------------------------------------------------------------------- |
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173 | \subsection[Closed, cyclic (\forcode{jperio = [0127]})] |
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174 | {Closed, cyclic (\protect\jp{jperio}\forcode{ = [0127]})} |
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175 | \label{subsec:LBC_jperio012} |
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176 | |
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177 | The choice of closed or cyclic model domain boundary condition is made by |
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178 | setting \jp{jperio} to 0, 1, 2 or 7 in namelist \nam{cfg}. |
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179 | Each time such a boundary condition is needed, it is set by a call to routine \mdl{lbclnk}. |
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180 | The computation of momentum and tracer trends proceeds from $i=2$ to $i=jpi-1$ and from $j=2$ to $j=jpj-1$, |
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181 | \ie\ in the model interior. |
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182 | To choose a lateral model boundary condition is to specify the first and last rows and columns of |
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183 | the model variables. |
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184 | |
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185 | \begin{description} |
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186 | |
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187 | \item[For closed boundary (\jp{jperio}\forcode{ = 0})], |
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188 | solid walls are imposed at all model boundaries: |
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189 | first and last rows and columns are set to zero. |
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190 | |
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191 | \item[For cyclic east-west boundary (\jp{jperio}\forcode{ = 1})], |
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192 | first and last rows are set to zero (closed) whilst the first column is set to |
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193 | the value of the last-but-one column and the last column to the value of the second one |
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194 | (\autoref{fig:LBC_jperio}-a). |
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195 | Whatever flows out of the eastern (western) end of the basin enters the western (eastern) end. |
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196 | |
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197 | \item[For cyclic north-south boundary (\jp{jperio}\forcode{ = 2})], |
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198 | first and last columns are set to zero (closed) whilst the first row is set to |
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199 | the value of the last-but-one row and the last row to the value of the second one |
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200 | (\autoref{fig:LBC_jperio}-a). |
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201 | Whatever flows out of the northern (southern) end of the basin enters the southern (northern) end. |
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202 | |
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203 | \item[Bi-cyclic east-west and north-south boundary (\jp{jperio}\forcode{ = 7})] combines cases 1 and 2. |
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204 | |
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205 | \end{description} |
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206 | |
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207 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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208 | \begin{figure}[!t] |
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209 | \begin{center} |
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210 | \includegraphics[width=\textwidth]{Fig_LBC_jperio} |
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211 | \caption{ |
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212 | \protect\label{fig:LBC_jperio} |
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213 | setting of (a) east-west cyclic (b) symmetric across the equator boundary conditions. |
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214 | } |
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215 | \end{center} |
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216 | \end{figure} |
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217 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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218 | |
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219 | % ------------------------------------------------------------------------------------------------------------- |
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220 | % North fold (\textit{jperio = 3 }to $6)$ |
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221 | % ------------------------------------------------------------------------------------------------------------- |
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222 | \subsection[North-fold (\forcode{jperio = [3-6]})] |
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223 | {North-fold (\protect\jp{jperio}\forcode{ = [3-6]})} |
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224 | \label{subsec:LBC_north_fold} |
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225 | |
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226 | The north fold boundary condition has been introduced in order to handle the north boundary of |
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227 | a three-polar ORCA grid. |
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228 | Such a grid has two poles in the northern hemisphere (\autoref{fig:MISC_ORCA_msh}, |
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229 | and thus requires a specific treatment illustrated in \autoref{fig:North_Fold_T}. |
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230 | Further information can be found in \mdl{lbcnfd} module which applies the north fold boundary condition. |
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231 | |
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232 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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233 | \begin{figure}[!t] |
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234 | \begin{center} |
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235 | \includegraphics[width=\textwidth]{Fig_North_Fold_T} |
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236 | \caption{ |
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237 | \protect\label{fig:North_Fold_T} |
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238 | North fold boundary with a $T$-point pivot and cyclic east-west boundary condition ($jperio=4$), |
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239 | as used in ORCA 2, 1/4, and 1/12. |
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240 | Pink shaded area corresponds to the inner domain mask (see text). |
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241 | } |
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242 | \end{center} |
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243 | \end{figure} |
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244 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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245 | |
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246 | % ==================================================================== |
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247 | % Exchange with neighbouring processors |
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248 | % ==================================================================== |
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249 | \section[Exchange with neighbouring processors (\textit{lbclnk.F90}, \textit{lib\_mpp.F90})] |
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250 | {Exchange with neighbouring processors (\protect\mdl{lbclnk}, \protect\mdl{lib\_mpp})} |
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251 | \label{sec:LBC_mpp} |
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252 | |
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253 | For massively parallel processing (mpp), a domain decomposition method is used. |
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254 | The basic idea of the method is to split the large computation domain of a numerical experiment into |
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255 | several smaller domains and solve the set of equations by addressing independent local problems. |
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256 | Each processor has its own local memory and computes the model equation over a subdomain of the whole model domain. |
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257 | The subdomain boundary conditions are specified through communications between processors which |
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258 | are organized by explicit statements (message passing method). |
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259 | |
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260 | A big advantage is that the method does not need many modifications of the initial \fortran code. |
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261 | From the modeller's point of view, each sub domain running on a processor is identical to the "mono-domain" code. |
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262 | In addition, the programmer manages the communications between subdomains, |
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263 | and the code is faster when the number of processors is increased. |
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264 | The porting of OPA code on an iPSC860 was achieved during Guyon's PhD [Guyon et al. 1994, 1995] |
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265 | in collaboration with CETIIS and ONERA. |
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266 | The implementation in the operational context and the studies of performance on |
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267 | a T3D and T3E Cray computers have been made in collaboration with IDRIS and CNRS. |
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268 | The present implementation is largely inspired by Guyon's work [Guyon 1995]. |
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269 | |
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270 | The parallelization strategy is defined by the physical characteristics of the ocean model. |
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271 | Second order finite difference schemes lead to local discrete operators that |
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272 | depend at the very most on one neighbouring point. |
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273 | The only non-local computations concern the vertical physics |
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274 | (implicit diffusion, turbulent closure scheme, ...) (delocalization over the whole water column), |
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275 | and the solving of the elliptic equation associated with the surface pressure gradient computation |
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276 | (delocalization over the whole horizontal domain). |
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277 | Therefore, a pencil strategy is used for the data sub-structuration: |
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278 | the 3D initial domain is laid out on local processor memories following a 2D horizontal topological splitting. |
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279 | Each sub-domain computes its own surface and bottom boundary conditions and |
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280 | has a side wall overlapping interface which defines the lateral boundary conditions for |
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281 | computations in the inner sub-domain. |
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282 | The overlapping area consists of the two rows at each edge of the sub-domain. |
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283 | After a computation, a communication phase starts: |
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284 | each processor sends to its neighbouring processors the update values of the points corresponding to |
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285 | the interior overlapping area to its neighbouring sub-domain (\ie\ the innermost of the two overlapping rows). |
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286 | The communication is done through the Message Passing Interface (MPI). |
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287 | The data exchanges between processors are required at the very place where |
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288 | lateral domain boundary conditions are set in the mono-domain computation: |
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289 | the \rou{lbc\_lnk} routine (found in \mdl{lbclnk} module) which manages such conditions is interfaced with |
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290 | routines found in \mdl{lib\_mpp} module when running on an MPP computer (\ie\ when \key{mpp\_mpi} defined). |
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291 | It has to be pointed out that when using the MPP version of the model, |
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292 | the east-west cyclic boundary condition is done implicitly, |
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293 | whilst the south-symmetric boundary condition option is not available. |
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294 | |
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295 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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296 | \begin{figure}[!t] |
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297 | \begin{center} |
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298 | \includegraphics[width=\textwidth]{Fig_mpp} |
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299 | \caption{ |
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300 | \protect\label{fig:mpp} |
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301 | Positioning of a sub-domain when massively parallel processing is used. |
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302 | } |
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303 | \end{center} |
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304 | \end{figure} |
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305 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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306 | |
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307 | In the standard version of \NEMO, the splitting is regular and arithmetic. |
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308 | The i-axis is divided by \jp{jpni} and |
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309 | the j-axis by \jp{jpnj} for a number of processors \jp{jpnij} most often equal to $jpni \times jpnj$ |
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310 | (parameters set in \nam{mpp} namelist). |
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311 | Each processor is independent and without message passing or synchronous process, |
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312 | programs run alone and access just its own local memory. |
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313 | For this reason, the main model dimensions are now the local dimensions of the subdomain (pencil) that |
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314 | are named \jp{jpi}, \jp{jpj}, \jp{jpk}. |
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315 | These dimensions include the internal domain and the overlapping rows. |
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316 | The number of rows to exchange (known as the halo) is usually set to one (\jp{jpreci}=1, in \mdl{par\_oce}). |
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317 | The whole domain dimensions are named \jp{jpiglo}, \jp{jpjglo} and \jp{jpk}. |
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318 | The relationship between the whole domain and a sub-domain is: |
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319 | \[ |
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320 | jpi = ( jpiglo-2*jpreci + (jpni-1) ) / jpni + 2*jpreci |
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321 | jpj = ( jpjglo-2*jprecj + (jpnj-1) ) / jpnj + 2*jprecj |
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322 | \] |
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323 | where \jp{jpni}, \jp{jpnj} are the number of processors following the i- and j-axis. |
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324 | |
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325 | One also defines variables nldi and nlei which correspond to the internal domain bounds, |
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326 | and the variables nimpp and njmpp which are the position of the (1,1) grid-point in the global domain. |
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327 | An element of $T_{l}$, a local array (subdomain) corresponds to an element of $T_{g}$, |
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328 | a global array (whole domain) by the relationship: |
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329 | \[ |
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330 | % \label{eq:lbc_nimpp} |
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331 | T_{g} (i+nimpp-1,j+njmpp-1,k) = T_{l} (i,j,k), |
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332 | \] |
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333 | with $1 \leq i \leq jpi$, $1 \leq j \leq jpj $ , and $1 \leq k \leq jpk$. |
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334 | |
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335 | Processors are numbered from 0 to $jpnij-1$, the number is saved in the variable nproc. |
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336 | In the standard version, a processor has no more than |
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337 | four neighbouring processors named nono (for north), noea (east), noso (south) and nowe (west) and |
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338 | two variables, nbondi and nbondj, indicate the relative position of the processor: |
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339 | \begin{itemize} |
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340 | \item nbondi = -1 an east neighbour, no west processor, |
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341 | \item nbondi = 0 an east neighbour, a west neighbour, |
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342 | \item nbondi = 1 no east processor, a west neighbour, |
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343 | \item nbondi = 2 no splitting following the i-axis. |
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344 | \end{itemize} |
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345 | During the simulation, processors exchange data with their neighbours. |
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346 | If there is effectively a neighbour, the processor receives variables from this processor on its overlapping row, |
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347 | and sends the data issued from internal domain corresponding to the overlapping row of the other processor. |
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348 | |
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349 | |
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350 | The \NEMO\ model computes equation terms with the help of mask arrays (0 on land points and 1 on sea points). |
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351 | It is easily readable and very efficient in the context of a computer with vectorial architecture. |
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352 | However, in the case of a scalar processor, computations over the land regions become more expensive in |
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353 | terms of CPU time. |
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354 | It is worse when we use a complex configuration with a realistic bathymetry like the global ocean where |
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355 | more than 50 \% of points are land points. |
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356 | For this reason, a pre-processing tool can be used to choose the mpp domain decomposition with a maximum number of |
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357 | only land points processors, which can then be eliminated (\autoref{fig:mppini2}) |
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358 | (For example, the mpp\_optimiz tools, available from the DRAKKAR web site). |
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359 | This optimisation is dependent on the specific bathymetry employed. |
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360 | The user then chooses optimal parameters \jp{jpni}, \jp{jpnj} and \jp{jpnij} with $jpnij < jpni \times jpnj$, |
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361 | leading to the elimination of $jpni \times jpnj - jpnij$ land processors. |
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362 | When those parameters are specified in \nam{mpp} namelist, |
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363 | the algorithm in the \rou{inimpp2} routine sets each processor's parameters (nbound, nono, noea,...) so that |
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364 | the land-only processors are not taken into account. |
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365 | |
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366 | \gmcomment{Note that the inimpp2 routine is general so that the original inimpp |
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367 | routine should be suppressed from the code.} |
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368 | |
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369 | When land processors are eliminated, |
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370 | the value corresponding to these locations in the model output files is undefined. |
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371 | Note that this is a problem for the meshmask file which requires to be defined over the whole domain. |
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372 | Therefore, user should not eliminate land processors when creating a meshmask file |
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373 | (\ie\ when setting a non-zero value to \np{nn\_msh}). |
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374 | |
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375 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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376 | \begin{figure}[!ht] |
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377 | \begin{center} |
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378 | \includegraphics[width=\textwidth]{Fig_mppini2} |
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379 | \caption { |
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380 | \protect\label{fig:mppini2} |
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381 | Example of Atlantic domain defined for the CLIPPER projet. |
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382 | Initial grid is composed of 773 x 1236 horizontal points. |
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383 | (a) the domain is split onto 9 \time 20 subdomains (jpni=9, jpnj=20). |
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384 | 52 subdomains are land areas. |
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385 | (b) 52 subdomains are eliminated (white rectangles) and |
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386 | the resulting number of processors really used during the computation is jpnij=128. |
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387 | } |
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388 | \end{center} |
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389 | \end{figure} |
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390 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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391 | |
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392 | |
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393 | % ==================================================================== |
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394 | % Unstructured open boundaries BDY |
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395 | % ==================================================================== |
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396 | \section{Unstructured open boundary conditions (BDY)} |
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397 | \label{sec:LBC_bdy} |
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398 | |
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399 | %-----------------------------------------nambdy-------------------------------------------- |
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400 | |
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401 | \nlst{nambdy} |
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402 | %----------------------------------------------------------------------------------------------- |
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403 | %-----------------------------------------nambdy_dta-------------------------------------------- |
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404 | |
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405 | \nlst{nambdy_dta} |
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406 | %----------------------------------------------------------------------------------------------- |
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407 | |
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408 | Options are defined through the \nam{bdy} \nam{bdy\_dta} namelist variables. |
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409 | The BDY module is the core implementation of open boundary conditions for regional configurations on |
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410 | temperature, salinity, barotropic and baroclinic velocities, as well as ice concentration, ice and snow thicknesses. |
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411 | |
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412 | The BDY module was modelled on the OBC module (see \NEMO\ 3.4) and shares many features and |
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413 | a similar coding structure \citep{chanut_rpt05}. |
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414 | The specification of the location of the open boundary is completely flexible and |
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415 | allows any type of setup, from regular boundaries to irregular contour (it includes the possibility to set an open boundary able to follow an isobath). |
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416 | Boundary data files used with versions of \NEMO\ prior to Version 3.4 may need to be re-ordered to work with this version. |
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417 | See the section on the Input Boundary Data Files for details. |
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418 | |
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419 | %---------------------------------------------- |
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420 | \subsection{Namelists} |
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421 | \label{subsec:BDY_namelist} |
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422 | |
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423 | The BDY module is activated by setting \np{ln\_bdy}\forcode{ = .true.} . |
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424 | It is possible to define more than one boundary ``set'' and apply different boundary conditions to each set. |
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425 | The number of boundary sets is defined by \np{nb\_bdy}. |
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426 | Each boundary set may be defined as a set of straight line segments in a namelist |
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427 | (\np{ln\_coords\_file}\forcode{ = .false.}) or read in from a file (\np{ln\_coords\_file}\forcode{ = .true.}). |
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428 | If the set is defined in a namelist, then the namelists \nam{bdy\_index} must be included separately, one for each set. |
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429 | If the set is defined by a file, then a ``\ifile{coordinates.bdy}'' file must be provided. |
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430 | The coordinates.bdy file is analagous to the usual \NEMO\ ``\ifile{coordinates}'' file. |
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431 | In the example above, there are two boundary sets, the first of which is defined via a file and |
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432 | the second is defined in a namelist. |
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433 | For more details of the definition of the boundary geometry see section \autoref{subsec:BDY_geometry}. |
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434 | |
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435 | For each boundary set a boundary condition has to be chosen for the barotropic solution |
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436 | (``u2d'':sea-surface height and barotropic velocities), for the baroclinic velocities (``u3d''), |
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437 | for the active tracers \footnote{The BDY module does not deal with passive tracers at this version} (``tra''), and sea-ice (``ice''). |
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438 | For each set of variables there is a choice of algorithm and a choice for the data, |
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439 | eg. for the active tracers the algorithm is set by \np{cn\_tra} and the choice of data is set by \np{nn\_tra\_dta}.\\ |
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440 | |
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441 | The choice of algorithm is currently as follows: |
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442 | |
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443 | \begin{description} |
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444 | \item[\forcode{'none'}:] No boundary condition applied. |
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445 | So the solution will ``see'' the land points around the edge of the edge of the domain. |
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446 | \item[\forcode{'specified'}:] Specified boundary condition applied (only available for baroclinic velocity and tracer variables). |
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447 | \item[\forcode{'neumann'}:] Value at the boundary are duplicated (No gradient). Only available for baroclinic velocity and tracer variables. |
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448 | \item[\forcode{'frs'}:] Flow Relaxation Scheme (FRS) available for all variables. |
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449 | \item[\forcode{'Orlanski'}:] Orlanski radiation scheme (fully oblique) for barotropic, baroclinic and tracer variables. |
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450 | \item[\forcode{'Orlanski_npo'}:] Orlanski radiation scheme for barotropic, baroclinic and tracer variables. |
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451 | \item[\forcode{'flather'}:] Flather radiation scheme for the barotropic variables only. |
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452 | \end{description} |
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453 | |
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454 | The main choice for the boundary data is to use initial conditions as boundary data |
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455 | (\np{nn\_tra\_dta}\forcode{ = 0}) or to use external data from a file (\np{nn\_tra\_dta}\forcode{ = 1}). |
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456 | In case the 3d velocity data contain the total velocity (ie, baroclinic and barotropic velocity), |
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457 | the bdy code can derived baroclinic and barotropic velocities by setting \np{ln\_full\_vel}\forcode{ = .true. } |
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458 | For the barotropic solution there is also the option to use tidal harmonic forcing either by |
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459 | itself (\np{nn\_dyn2d\_dta}\forcode{ = 2}) or in addition to other external data (\np{nn\_dyn2d\_dta}\forcode{ = 3}).\\ |
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460 | Sea-ice salinity, temperature and age data at the boundary are constant and defined repectively by \np{rn\_ice\_sal}, \np{rn\_ice\_tem} and \np{rn\_ice\_age}. |
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461 | |
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462 | If external boundary data is required then the \nam{bdy\_dta} namelist must be defined. |
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463 | One \nam{bdy\_dta} namelist is required for each boundary set, adopting the same order of indexes in which the boundary sets are defined in nambdy. |
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464 | In the example given, two boundary sets have been defined. The first one is reading data file in the \nam{bdy\_dta} namelist shown above |
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465 | and the second one is using data from intial condition (no namelist block needed). |
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466 | The boundary data is read in using the fldread module, |
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467 | so the \nam{bdy\_dta} namelist is in the format required for fldread. |
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468 | For each required variable, the filename, the frequency of the files and |
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469 | the frequency of the data in the files are given. |
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470 | Also whether or not time-interpolation is required and whether the data is climatological (time-cyclic) data.\\ |
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471 | |
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472 | There is currently an option to vertically interpolate the open boundary data onto the native grid at run-time. |
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473 | If \np{nn\_bdy\_jpk} $< -1$, it is assumed that the lateral boundary data are already on the native grid. |
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474 | However, if \np{nn\_bdy\_jpk} is set to the number of vertical levels present in the boundary data, |
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475 | a bilinear interpolation onto the native grid will be triggered at runtime. |
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476 | For this to be successful the additional variables: $gdept$, $gdepu$, $gdepv$, $e3t$, $e3u$ and $e3v$, are required to be present in the lateral boundary files. |
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477 | These correspond to the depths and scale factors of the input data, |
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478 | the latter used to make any adjustment to the velocity fields due to differences in the total water depths between the two vertical grids.\\ |
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479 | |
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480 | In the example of given namelists, two boundary sets are defined. |
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481 | The first set is defined via a file and applies FRS conditions to temperature and salinity and |
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482 | Flather conditions to the barotropic variables. No condition specified for the baroclinic velocity and sea-ice. |
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483 | External data is provided in daily files (from a large-scale model). |
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484 | Tidal harmonic forcing is also used. |
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485 | The second set is defined in a namelist. |
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486 | FRS conditions are applied on temperature and salinity and climatological data is read from initial condition files. |
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487 | |
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488 | %---------------------------------------------- |
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489 | \subsection{Flow relaxation scheme} |
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490 | \label{subsec:BDY_FRS_scheme} |
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491 | |
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492 | The Flow Relaxation Scheme (FRS) \citep{davies_QJRMS76,engedahl_T95}, |
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493 | applies a simple relaxation of the model fields to externally-specified values over |
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494 | a zone next to the edge of the model domain. |
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495 | Given a model prognostic variable $\Phi$ |
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496 | \[ |
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497 | % \label{eq:bdy_frs1} |
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498 | \Phi(d) = \alpha(d)\Phi_{e}(d) + (1-\alpha(d))\Phi_{m}(d)\;\;\;\;\; d=1,N |
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499 | \] |
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500 | where $\Phi_{m}$ is the model solution and $\Phi_{e}$ is the specified external field, |
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501 | $d$ gives the discrete distance from the model boundary and |
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502 | $\alpha$ is a parameter that varies from $1$ at $d=1$ to a small value at $d=N$. |
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503 | It can be shown that this scheme is equivalent to adding a relaxation term to |
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504 | the prognostic equation for $\Phi$ of the form: |
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505 | \[ |
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506 | % \label{eq:bdy_frs2} |
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507 | -\frac{1}{\tau}\left(\Phi - \Phi_{e}\right) |
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508 | \] |
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509 | where the relaxation time scale $\tau$ is given by a function of $\alpha$ and the model time step $\Delta t$: |
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510 | \[ |
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511 | % \label{eq:bdy_frs3} |
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512 | \tau = \frac{1-\alpha}{\alpha} \,\rdt |
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513 | \] |
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514 | Thus the model solution is completely prescribed by the external conditions at the edge of the model domain and |
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515 | is relaxed towards the external conditions over the rest of the FRS zone. |
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516 | The application of a relaxation zone helps to prevent spurious reflection of |
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517 | outgoing signals from the model boundary. |
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518 | |
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519 | The function $\alpha$ is specified as a $tanh$ function: |
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520 | \[ |
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521 | % \label{eq:bdy_frs4} |
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522 | \alpha(d) = 1 - \tanh\left(\frac{d-1}{2}\right), \quad d=1,N |
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523 | \] |
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524 | The width of the FRS zone is specified in the namelist as \np{nn\_rimwidth}. |
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525 | This is typically set to a value between 8 and 10. |
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526 | |
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527 | %---------------------------------------------- |
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528 | \subsection{Flather radiation scheme} |
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529 | \label{subsec:BDY_flather_scheme} |
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530 | |
---|
531 | The \citet{flather_JPO94} scheme is a radiation condition on the normal, |
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532 | depth-mean transport across the open boundary. |
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533 | It takes the form |
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534 | \begin{equation} \label{eq:bdy_fla1} |
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535 | U = U_{e} + \frac{c}{h}\left(\eta - \eta_{e}\right), |
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536 | \end{equation} |
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537 | where $U$ is the depth-mean velocity normal to the boundary and $\eta$ is the sea surface height, |
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538 | both from the model. |
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539 | The subscript $e$ indicates the same fields from external sources. |
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540 | The speed of external gravity waves is given by $c = \sqrt{gh}$, and $h$ is the depth of the water column. |
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541 | The depth-mean normal velocity along the edge of the model domain is set equal to |
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542 | the external depth-mean normal velocity, |
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543 | plus a correction term that allows gravity waves generated internally to exit the model boundary. |
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544 | Note that the sea-surface height gradient in \autoref{eq:bdy_fla1} is a spatial gradient across the model boundary, |
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545 | so that $\eta_{e}$ is defined on the $T$ points with $nbr=1$ and $\eta$ is defined on the $T$ points with $nbr=2$. |
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546 | $U$ and $U_{e}$ are defined on the $U$ or $V$ points with $nbr=1$, \ie\ between the two $T$ grid points. |
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547 | |
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548 | %---------------------------------------------- |
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549 | \subsection{Orlanski radiation scheme} |
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550 | \label{subsec:BDY_orlanski_scheme} |
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551 | |
---|
552 | The Orlanski scheme is based on the algorithm described by \citep{marchesiello.mcwilliams.ea_OM01}, hereafter MMS. |
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553 | |
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554 | The adaptive Orlanski condition solves a wave plus relaxation equation at the boundary: |
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555 | \begin{equation} |
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556 | \frac{\partial\phi}{\partial t} + c_x \frac{\partial\phi}{\partial x} + c_y \frac{\partial\phi}{\partial y} = |
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557 | -\frac{1}{\tau}(\phi - \phi^{ext}) |
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558 | \label{eq:wave_continuous} |
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559 | \end{equation} |
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560 | |
---|
561 | where $\phi$ is the model field, $x$ and $y$ refer to the normal and tangential directions to the boundary respectively, and the phase |
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562 | velocities are diagnosed from the model fields as: |
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563 | |
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564 | \begin{equation} \label{eq:cx} |
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565 | c_x = -\frac{\partial\phi}{\partial t}\frac{\partial\phi / \partial x}{(\partial\phi /\partial x)^2 + (\partial\phi /\partial y)^2} |
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566 | \end{equation} |
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567 | \begin{equation} |
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568 | \label{eq:cy} |
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569 | c_y = -\frac{\partial\phi}{\partial t}\frac{\partial\phi / \partial y}{(\partial\phi /\partial x)^2 + (\partial\phi /\partial y)^2} |
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570 | \end{equation} |
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571 | |
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572 | (As noted by MMS, this is a circular diagnosis of the phase speeds which only makes sense on a discrete grid). |
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573 | Equation (\autoref{eq:wave_continuous}) is defined adaptively depending on the sign of the phase velocity normal to the boundary $c_x$. |
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574 | For $c_x$ outward, we have |
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575 | |
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576 | \begin{equation} |
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577 | \tau = \tau_{out} |
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578 | \end{equation} |
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579 | |
---|
580 | For $c_x$ inward, the radiation equation is not applied: |
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581 | |
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582 | \begin{equation} |
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583 | \tau = \tau_{in}\,\,\,;\,\,\, c_x = c_y = 0 |
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584 | \label{eq:tau_in} |
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585 | \end{equation} |
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586 | |
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587 | Generally the relaxation time scale at inward propagation points (\np{rn\_time\_dmp}) is set much shorter than the time scale at outward propagation |
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588 | points (\np{rn\_time\_dmp\_out}) so that the solution is constrained more strongly by the external data at inward propagation points. |
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589 | See \autoref{subsec:BDY_relaxation} for detailed on the spatial shape of the scaling.\\ |
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590 | The ``normal propagation of oblique radiation'' or NPO approximation (called \forcode{'orlanski_npo'}) involves assuming |
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591 | that $c_y$ is zero in equation (\autoref{eq:wave_continuous}), but including |
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592 | this term in the denominator of equation (\autoref{eq:cx}). Both versions of the scheme are options in BDY. Equations |
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593 | (\autoref{eq:wave_continuous}) - (\autoref{eq:tau_in}) correspond to equations (13) - (15) and (2) - (3) in MMS.\\ |
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594 | |
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595 | %---------------------------------------------- |
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596 | \subsection{Relaxation at the boundary} |
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597 | \label{subsec:BDY_relaxation} |
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598 | |
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599 | In addition to a specific boundary condition specified as \np{cn\_tra} and \np{cn\_dyn3d}, relaxation on baroclinic velocities and tracers variables are available. |
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600 | It is control by the namelist parameter \np{ln\_tra\_dmp} and \np{ln\_dyn3d\_dmp} for each boundary set. |
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601 | |
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602 | The relaxation time scale value (\np{rn\_time\_dmp} and \np{rn\_time\_dmp\_out}, $\tau$) are defined at the boundaries itself. |
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603 | This time scale ($\alpha$) is weighted by the distance ($d$) from the boundary over \np{nn\_rimwidth} cells ($N$): |
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604 | |
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605 | \[ |
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606 | \alpha = \frac{1}{\tau}(\frac{N+1-d}{N})^2, \quad d=1,N |
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607 | \] |
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608 | |
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609 | The same scaling is applied in the Orlanski damping. |
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610 | |
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611 | %---------------------------------------------- |
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612 | \subsection{Boundary geometry} |
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613 | \label{subsec:BDY_geometry} |
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614 | |
---|
615 | Each open boundary set is defined as a list of points. |
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616 | The information is stored in the arrays $nbi$, $nbj$, and $nbr$ in the $idx\_bdy$ structure. |
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617 | The $nbi$ and $nbj$ arrays define the local $(i,j)$ indexes of each point in the boundary zone and |
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618 | the $nbr$ array defines the discrete distance from the boundary: $nbr=1$ means that |
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619 | the boundary point is next to the edge of the model domain, while $nbr>1$ means that |
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620 | the boundary point is increasingly further away from the edge of the model domain. |
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621 | A set of $nbi$, $nbj$, and $nbr$ arrays is defined for each of the $T$, $U$ and $V$ grids. |
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622 | Figure \autoref{fig:LBC_bdy_geom} shows an example of an irregular boundary. |
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623 | |
---|
624 | The boundary geometry for each set may be defined in a namelist nambdy\_index or |
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625 | by reading in a ``\ifile{coordinates.bdy}'' file. |
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626 | The nambdy\_index namelist defines a series of straight-line segments for north, east, south and west boundaries. |
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627 | One nambdy\_index namelist block is needed for each boundary condition defined by indexes. |
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628 | For the northern boundary, \texttt{nbdysegn} gives the number of segments, |
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629 | \jp{jpjnob} gives the $j$ index for each segment and \jp{jpindt} and |
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630 | \jp{jpinft} give the start and end $i$ indices for each segment with similar for the other boundaries. |
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631 | These segments define a list of $T$ grid points along the outermost row of the boundary ($nbr\,=\, 1$). |
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632 | The code deduces the $U$ and $V$ points and also the points for $nbr\,>\, 1$ if \np{nn\_rimwidth}\forcode{ > 1}. |
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633 | |
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634 | The boundary geometry may also be defined from a ``\ifile{coordinates.bdy}'' file. |
---|
635 | Figure \autoref{fig:LBC_nc_header} gives an example of the header information from such a file, based on the description of geometrical setup given above. |
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636 | The file should contain the index arrays for each of the $T$, $U$ and $V$ grids. |
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637 | The arrays must be in order of increasing $nbr$. |
---|
638 | Note that the $nbi$, $nbj$ values in the file are global values and are converted to local values in the code. |
---|
639 | Typically this file will be used to generate external boundary data via interpolation and so |
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640 | will also contain the latitudes and longitudes of each point as shown. |
---|
641 | However, this is not necessary to run the model. |
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642 | |
---|
643 | For some choices of irregular boundary the model domain may contain areas of ocean which |
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644 | are not part of the computational domain. |
---|
645 | For example, if an open boundary is defined along an isobath, say at the shelf break, |
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646 | then the areas of ocean outside of this boundary will need to be masked out. |
---|
647 | This can be done by reading a mask file defined as \np{cn\_mask\_file} in the nam\_bdy namelist. |
---|
648 | Only one mask file is used even if multiple boundary sets are defined. |
---|
649 | |
---|
650 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
651 | \begin{figure}[!t] |
---|
652 | \begin{center} |
---|
653 | \includegraphics[width=\textwidth]{Fig_LBC_bdy_geom} |
---|
654 | \caption { |
---|
655 | \protect\label{fig:LBC_bdy_geom} |
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656 | Example of geometry of unstructured open boundary |
---|
657 | } |
---|
658 | \end{center} |
---|
659 | \end{figure} |
---|
660 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
661 | |
---|
662 | %---------------------------------------------- |
---|
663 | \subsection{Input boundary data files} |
---|
664 | \label{subsec:BDY_data} |
---|
665 | |
---|
666 | The data files contain the data arrays in the order in which the points are defined in the $nbi$ and $nbj$ arrays. |
---|
667 | The data arrays are dimensioned on: |
---|
668 | a time dimension; |
---|
669 | $xb$ which is the index of the boundary data point in the horizontal; |
---|
670 | and $yb$ which is a degenerate dimension of 1 to enable the file to be read by the standard \NEMO\ I/O routines. |
---|
671 | The 3D fields also have a depth dimension. |
---|
672 | |
---|
673 | From Version 3.4 there are new restrictions on the order in which the boundary points are defined |
---|
674 | (and therefore restrictions on the order of the data in the file). |
---|
675 | In particular: |
---|
676 | |
---|
677 | \begin{enumerate} |
---|
678 | \item The data points must be in order of increasing $nbr$, |
---|
679 | ie. all the $nbr=1$ points, then all the $nbr=2$ points etc. |
---|
680 | \item All the data for a particular boundary set must be in the same order. |
---|
681 | (Prior to 3.4 it was possible to define barotropic data in a different order to |
---|
682 | the data for tracers and baroclinic velocities). |
---|
683 | \end{enumerate} |
---|
684 | |
---|
685 | These restrictions mean that data files used with versions of the |
---|
686 | model prior to Version 3.4 may not work with Version 3.4 onwards. |
---|
687 | A \fortran utility {\itshape bdy\_reorder} exists in the TOOLS directory which |
---|
688 | will re-order the data in old BDY data files. |
---|
689 | |
---|
690 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
691 | \begin{figure}[!t] |
---|
692 | \begin{center} |
---|
693 | \includegraphics[width=\textwidth]{Fig_LBC_nc_header} |
---|
694 | \caption { |
---|
695 | \protect\label{fig:LBC_nc_header} |
---|
696 | Example of the header for a \protect\ifile{coordinates.bdy} file |
---|
697 | } |
---|
698 | \end{center} |
---|
699 | \end{figure} |
---|
700 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
---|
701 | |
---|
702 | %---------------------------------------------- |
---|
703 | \subsection{Volume correction} |
---|
704 | \label{subsec:BDY_vol_corr} |
---|
705 | |
---|
706 | There is an option to force the total volume in the regional model to be constant. |
---|
707 | This is controlled by the \np{ln\_vol} parameter in the namelist. |
---|
708 | A value of \np{ln\_vol}\forcode{ = .false.} indicates that this option is not used. |
---|
709 | Two options to control the volume are available (\np{nn\_volctl}). |
---|
710 | If \np{nn\_volctl}\forcode{ = 0} then a correction is applied to the normal barotropic velocities around the boundary at |
---|
711 | each timestep to ensure that the integrated volume flow through the boundary is zero. |
---|
712 | If \np{nn\_volctl}\forcode{ = 1} then the calculation of the volume change on |
---|
713 | the timestep includes the change due to the freshwater flux across the surface and |
---|
714 | the correction velocity corrects for this as well. |
---|
715 | |
---|
716 | If more than one boundary set is used then volume correction is |
---|
717 | applied to all boundaries at once. |
---|
718 | |
---|
719 | %---------------------------------------------- |
---|
720 | \subsection{Tidal harmonic forcing} |
---|
721 | \label{subsec:BDY_tides} |
---|
722 | |
---|
723 | %-----------------------------------------nambdy_tide-------------------------------------------- |
---|
724 | |
---|
725 | \nlst{nambdy_tide} |
---|
726 | %----------------------------------------------------------------------------------------------- |
---|
727 | |
---|
728 | Tidal forcing at open boundaries requires the activation of surface |
---|
729 | tides (i.e., in \nam{\_tide}, \np{ln\_tide} needs to be set to |
---|
730 | \forcode{.true.} and the required constituents need to be activated by |
---|
731 | including their names in the \np{clname} array; see |
---|
732 | \autoref{sec:SBC_tide}). Specific options related to the reading in of |
---|
733 | the complex harmonic amplitudes of elevation (SSH) and barotropic |
---|
734 | velocity (u,v) at open boundaries are defined through the |
---|
735 | \nam{bdy\_tide} namelist parameters.\\ |
---|
736 | |
---|
737 | The tidal harmonic data at open boundaries can be specified in two |
---|
738 | different ways, either on a two-dimensional grid covering the entire |
---|
739 | model domain or along open boundary segments; these two variants can |
---|
740 | be selected by setting \np{ln\_bdytide\_2ddta } to \forcode{.true.} or |
---|
741 | \forcode{.false.}, respectively. In either case, the real and |
---|
742 | imaginary parts of SSH and the two barotropic velocity components for |
---|
743 | each activated tidal constituent \textit{tcname} have to be provided |
---|
744 | separately: when two-dimensional data is used, variables |
---|
745 | \textit{tcname\_z1} and \textit{tcname\_z2} for real and imaginary SSH, |
---|
746 | respectively, are expected in input file \np{filtide} with suffix |
---|
747 | \ifile{\_grid\_T}, variables \textit{tcname\_u1} and |
---|
748 | \textit{tcname\_u2} for real and imaginary u, respectively, are |
---|
749 | expected in input file \np{filtide} with suffix \ifile{\_grid\_U}, and |
---|
750 | \textit{tcname\_v1} and \textit{tcname\_v2} for real and imaginary v, |
---|
751 | respectively, are expected in input file \np{filtide} with suffix |
---|
752 | \ifile{\_grid\_V}; when data along open boundary segments is used, |
---|
753 | variables \textit{z1} and \textit{z2} (real and imaginary part of SSH) |
---|
754 | are expected to be available from file \np{filtide} with suffix |
---|
755 | \ifile{tcname\_grid\_T}, variables \textit{u1} and \textit{u2} (real |
---|
756 | and imaginary part of u) are expected to be available from file |
---|
757 | \np{filtide} with suffix \ifile{tcname\_grid\_U}, and variables |
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758 | \textit{v1} and \textit{v2} (real and imaginary part of v) are |
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759 | expected to be available from file \np{filtide} with suffix |
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760 | \ifile{tcname\_grid\_V}. If \np{ln\_bdytide\_conj} is set to |
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761 | \forcode{.true.}, the data is expected to be in complex conjugate |
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762 | form. |
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763 | |
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764 | Note that the barotropic velocity components are assumed to be defined |
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765 | on the native model grid and should be rotated accordingly when they |
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766 | are converted from their definition on a different source grid. To do |
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767 | so, the u, v amplitudes and phases can be converted into tidal |
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768 | ellipses, the grid rotation added to the ellipse inclination, and then |
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769 | converted back (care should be taken regarding conventions of the |
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770 | direction of rotation). %, e.g. anticlockwise or clockwise. |
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771 | |
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772 | \biblio |
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773 | |
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774 | \pindex |
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775 | |
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776 | \end{document} |
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