1 | #LyX 2.2 created this file. For more info see http://www.lyx.org/ |
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2 | \lyxformat 508 |
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3 | \begin_document |
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4 | \begin_header |
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7 | \textclass book |
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8 | \use_default_options true |
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9 | \master ../../XIOS_user_guide.lyx |
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11 | \language english |
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55 | \index Index |
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56 | \shortcut idx |
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57 | \color #008000 |
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58 | \end_index |
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59 | \secnumdepth 3 |
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60 | \tocdepth 3 |
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61 | \paragraph_separation indent |
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62 | \paragraph_indentation default |
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63 | \quotes_language english |
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72 | \end_header |
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73 | |
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74 | \begin_body |
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75 | |
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76 | \begin_layout Chapter |
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77 | Grid |
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78 | \end_layout |
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79 | |
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80 | \begin_layout Section |
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81 | Overview |
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82 | \end_layout |
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83 | |
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84 | \begin_layout Standard |
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85 | Grid plays an important role in XIOS. |
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86 | Same as Field, Grid is one of the basic elements in XIOS, which should |
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87 | be well defined, not only in the configuration file but also in the FORTRAN |
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88 | code. |
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89 | Because, until now, XIOS has mainly served for writing NetCDF data format, |
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90 | most of its components are inspired from NetCDF Data Model, and Grid is |
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91 | not an exception. |
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92 | Grid is a concept describing dimensions that contain the axes of the data |
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93 | arrays. |
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94 | Moreover, Grid always consists of an unlimited dimension whose length can |
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95 | be expanded at any time. |
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96 | Other dimensions can be described with Domain and Axis. |
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97 | The followings describe how to make use of Grid in XIOS. |
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98 | Details of its attributes and operations can be found in XIOS reference |
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99 | guide. |
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100 | \end_layout |
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101 | |
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102 | \begin_layout Section |
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103 | Working with configuration file |
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104 | \end_layout |
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105 | |
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106 | \begin_layout Standard |
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107 | As mentioned above, a grid contains the axes of the data arrays, which are |
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108 | characterized by Domain and/or Axis. |
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109 | A domain is composed of a 2-dimension array, meanwhile an axis is, as its |
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110 | name, an 1-dimension array. |
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111 | |
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112 | \end_layout |
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113 | |
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114 | \begin_layout Standard |
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115 | Like other components of XIOS, a grid is defined inside its definition part |
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116 | with the tag |
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117 | \series bold |
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118 | \color black |
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119 | grid_definition |
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120 | \series default |
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121 | \color inherit |
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122 | |
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123 | \begin_inset listings |
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124 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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125 | inline false |
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126 | status collapsed |
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127 | |
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128 | \begin_layout Plain Layout |
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129 | |
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130 | <grid_definition> |
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131 | \end_layout |
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132 | |
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133 | \begin_layout Plain Layout |
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134 | |
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135 | <grid_group id="gridGroup"> |
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136 | \end_layout |
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137 | |
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138 | \begin_layout Plain Layout |
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139 | |
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140 | <grid id="grid_A"> |
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141 | \end_layout |
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142 | |
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143 | \begin_layout Plain Layout |
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144 | |
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145 | <domain domain_ref="domain_A" /> |
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146 | \end_layout |
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147 | |
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148 | \begin_layout Plain Layout |
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149 | |
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150 | <axis axis_ref="axis_C" /> |
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151 | \end_layout |
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152 | |
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153 | \begin_layout Plain Layout |
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154 | |
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155 | </grid> |
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156 | \end_layout |
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157 | |
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158 | \begin_layout Plain Layout |
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159 | |
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160 | <grid id="grid_Axis"> |
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161 | \end_layout |
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162 | |
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163 | \begin_layout Plain Layout |
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164 | |
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165 | <axis axis_ref="axis_D" /> |
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166 | \end_layout |
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167 | |
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168 | \begin_layout Plain Layout |
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169 | |
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170 | </grid> |
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171 | \end_layout |
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172 | |
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173 | \begin_layout Plain Layout |
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174 | |
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175 | <grid id="grid_All_Axis"> |
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176 | \end_layout |
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177 | |
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178 | \begin_layout Plain Layout |
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179 | |
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180 | <axis axis_ref="axis_A" /> |
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181 | \end_layout |
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182 | |
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183 | \begin_layout Plain Layout |
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184 | |
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185 | <axis axis_ref="axis_B" /> |
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186 | \end_layout |
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187 | |
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188 | \begin_layout Plain Layout |
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189 | |
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190 | <axis axis_ref="axis_C" /> |
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191 | \end_layout |
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192 | |
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193 | \begin_layout Plain Layout |
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194 | |
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195 | </grid> |
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196 | \end_layout |
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197 | |
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198 | \begin_layout Plain Layout |
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199 | |
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200 | </grid_group> |
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201 | \end_layout |
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202 | |
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203 | \begin_layout Plain Layout |
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204 | |
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205 | </grid_definition> |
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206 | \end_layout |
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207 | |
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208 | \end_inset |
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209 | |
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210 | |
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211 | \end_layout |
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212 | |
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213 | \begin_layout Standard |
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214 | As XIOS supports netCDF-4/HDF5, it allows user to gather several grids into |
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215 | groups to better organize data. |
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216 | Very often, grids are grouped, basing on the dimensions that they describe. |
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217 | However, there is not a limit for user to group out the grids. |
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218 | The more important thing than grid_group is grid. |
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219 | A grid is defined with the tag |
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220 | \series bold |
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221 | \color black |
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222 | grid. |
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223 | |
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224 | \end_layout |
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225 | |
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226 | \begin_layout Standard |
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227 | While it is not crucial for a grid group not to have an identification specified |
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228 | by attribute id, a grid must be assigned an id to become useful. |
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229 | Unlike grid group is a way of hierarchically organizing related grid only, |
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230 | a grid itself is referenced by fields with its id. |
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231 | Without the id, a grid can not be made used of by a field. |
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232 | Id is a string of anything but there is one thing to remember: id of a |
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233 | grid as well as id of any component in XIOS are |
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234 | \shape italic |
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235 | \color black |
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236 | unique |
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237 | \shape default |
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238 | \color inherit |
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239 | among this kind of components. |
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240 | If several grids use same Id, they all represent only one grid. |
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241 | \end_layout |
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242 | |
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243 | \begin_layout Standard |
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244 | A grid is defined by domain(s) and axis. |
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245 | A domain represents two-dimension data while an axis serves as one-dimension |
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246 | data. |
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247 | They are defined inside the grid definition. |
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248 | One of the convenient and effective way to reuse the definitions in XIOS |
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249 | is to take advantage of attribute *_ref. |
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250 | On using *_ref, the referencing component has all attributes from its reference |
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251 | d one. |
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252 | As the example below, grid with id |
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253 | \begin_inset Quotes eld |
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254 | \end_inset |
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255 | |
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256 | grid_A |
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257 | \begin_inset Quotes erd |
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258 | \end_inset |
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259 | |
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260 | (from now one, called grid_A), is composed of one domain whose attributes |
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261 | derived directly from another one-domain_A, and one axis whose attributes |
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262 | are taken from axis axis_C, which are defined previously. |
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263 | \end_layout |
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264 | |
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265 | \begin_layout Standard |
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266 | \begin_inset listings |
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267 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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268 | inline false |
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269 | status open |
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270 | |
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271 | \begin_layout Plain Layout |
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272 | |
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273 | <domain id="domain_A /> |
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274 | \end_layout |
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275 | |
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276 | \begin_layout Plain Layout |
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277 | |
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278 | <axis id="axis_A" /> |
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279 | \end_layout |
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280 | |
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281 | \begin_layout Plain Layout |
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282 | |
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283 | \end_layout |
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284 | |
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285 | \begin_layout Plain Layout |
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286 | |
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287 | <grid id="grid_A"> |
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288 | \end_layout |
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289 | |
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290 | \begin_layout Plain Layout |
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291 | |
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292 | <domain domain_ref="domain_A" /> |
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293 | \end_layout |
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294 | |
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295 | \begin_layout Plain Layout |
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296 | |
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297 | <axis axis_ref="axis_C" /> |
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298 | \end_layout |
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299 | |
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300 | \begin_layout Plain Layout |
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301 | |
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302 | </grid> |
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303 | \end_layout |
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304 | |
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305 | \end_inset |
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306 | |
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307 | |
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308 | \end_layout |
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309 | |
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310 | \begin_layout Standard |
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311 | The *_ref can only used to reference to a already defined element (e.g domain, |
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312 | axis, grid, etc). |
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313 | If these *_ref have not been defined yet, there will be a runtime error. |
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314 | \end_layout |
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315 | |
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316 | \begin_layout Standard |
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317 | Details about domain and axis can be found in other sections but there is |
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318 | one thing to bear in mind: A domain represents two-dimension data and it |
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319 | also contains several special information: longitude, latitude, bound, |
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320 | etc. |
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321 | For the meteorological mind, domain indicates a surface with latitude and |
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322 | longitude, whereas axis represents a vertical level. |
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323 | |
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324 | \end_layout |
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325 | |
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326 | \begin_layout Standard |
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327 | In general cases, there is only a need of writing some multidimensional |
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328 | data to a netCDF without any specific information, then comes the following |
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329 | definition of grid. |
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330 | \end_layout |
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331 | |
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332 | \begin_layout Standard |
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333 | \begin_inset listings |
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334 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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335 | inline false |
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336 | status open |
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337 | |
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338 | \begin_layout Plain Layout |
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339 | |
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340 | <grid id="grid_All_Axis"> |
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341 | \end_layout |
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342 | |
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343 | \begin_layout Plain Layout |
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344 | |
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345 | <axis axis_ref="axis_A" /> |
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346 | \end_layout |
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347 | |
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348 | \begin_layout Plain Layout |
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349 | |
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350 | <axis axis_ref="axis_B" /> |
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351 | \end_layout |
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352 | |
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353 | \begin_layout Plain Layout |
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354 | |
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355 | <axis axis_ref="axis_C" /> |
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356 | \end_layout |
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357 | |
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358 | \begin_layout Plain Layout |
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359 | |
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360 | </grid> |
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361 | \end_layout |
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362 | |
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363 | \end_inset |
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364 | |
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365 | |
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366 | \end_layout |
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367 | |
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368 | \begin_layout Standard |
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369 | The grid_All_Axis is similar to grid_A, but with three dimensions defined |
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370 | by 3 axis that can be described in any way on demand of user. |
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371 | For example, the axis_A and the axis_B can have corresponding name latitude |
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372 | and longitude to characterize a two-dimension surface with latitude and |
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373 | longitude. |
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374 | \end_layout |
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375 | |
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376 | \begin_layout Standard |
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377 | Very often, one dimensional data needs writing to netCDF, it can be easily |
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378 | done with the following XML code |
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379 | \end_layout |
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380 | |
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381 | \begin_layout Standard |
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382 | \begin_inset listings |
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383 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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384 | inline false |
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385 | status open |
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386 | |
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387 | \begin_layout Plain Layout |
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388 | |
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389 | <grid id="grid_Axis"> |
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390 | \end_layout |
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391 | |
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392 | \begin_layout Plain Layout |
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393 | |
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394 | <axis axis_ref="axis_D" /> |
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395 | \end_layout |
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396 | |
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397 | \begin_layout Plain Layout |
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398 | |
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399 | </grid> |
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400 | \end_layout |
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401 | |
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402 | \end_inset |
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403 | |
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404 | |
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405 | \end_layout |
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406 | |
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407 | \begin_layout Standard |
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408 | As it is discussed more details in the next section, but remember that even |
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409 | the non-distributed one dimensional data can be well processed by XIOS. |
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410 | |
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411 | \end_layout |
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412 | |
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413 | \begin_layout Standard |
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414 | As mentioned above, grid includes by default one unlimited dimension which |
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415 | is often used as time step axis. |
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416 | In order to write only time step to netCDF, XIOS provides a special way |
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417 | to do: scalar grid - a grid composed of a scalar |
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418 | \end_layout |
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419 | |
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420 | \begin_layout Standard |
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421 | \begin_inset listings |
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422 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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423 | inline false |
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424 | status open |
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425 | |
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426 | \begin_layout Plain Layout |
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427 | |
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428 | <grid id="grid_TimeStep"> |
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429 | \end_layout |
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430 | |
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431 | \begin_layout Plain Layout |
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432 | |
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433 | <scalar id="scalar" /> |
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434 | \end_layout |
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435 | |
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436 | \begin_layout Plain Layout |
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437 | |
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438 | </grid> |
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439 | \end_layout |
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440 | |
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441 | \end_inset |
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442 | |
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443 | |
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444 | \end_layout |
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445 | |
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446 | \begin_layout Standard |
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447 | âThe order of domain and/or in grid definition decides order of data written |
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448 | to netCDF: data on domain or axis appearing firstly in grid definition |
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449 | will vary the most. |
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450 | For example, on using ncdump command on netCDF which contains data written |
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451 | on the grid_A . |
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452 | \end_layout |
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453 | |
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454 | \begin_layout Standard |
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455 | \begin_inset listings |
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456 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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457 | inline false |
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458 | status open |
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459 | |
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460 | \begin_layout Plain Layout |
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461 | |
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462 | float field_A(time_counter, axis_A, y, x) ; |
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463 | \end_layout |
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464 | |
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465 | \begin_layout Plain Layout |
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466 | |
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467 | field_A:online_operation = "average" ; |
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468 | \end_layout |
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469 | |
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470 | \begin_layout Plain Layout |
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471 | |
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472 | field_A:interval_operation = "3600s" ; |
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473 | \end_layout |
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474 | |
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475 | \begin_layout Plain Layout |
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476 | |
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477 | field_A:interval_write = "6h" ; |
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478 | \end_layout |
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479 | |
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480 | \begin_layout Plain Layout |
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481 | |
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482 | field_A:coordinates = "time_centered axis_A nav_lat nav_lon" ; |
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483 | \end_layout |
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484 | |
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485 | \end_inset |
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486 | |
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487 | |
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488 | \end_layout |
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489 | |
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490 | \begin_layout Standard |
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491 | The data vary most quickly on dimension y, x which are two axes of domain_A. |
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492 | These are the default name of these dimension of a domain. |
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493 | The data on axis_C vary slower than on the domain and all the data are |
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494 | written one time step defined by time_counter at a time. |
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495 | \end_layout |
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496 | |
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497 | \begin_layout Standard |
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498 | Although a grid can be easily configured in XML file, it also needs defining |
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499 | in the FORTRAN via the definition of domain and axis for a model to work |
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500 | fully and correctly. |
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501 | All these instruction will be detailed in the next section. |
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502 | \end_layout |
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503 | |
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504 | \begin_layout Section |
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505 | Working with FORTRAN code |
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506 | \end_layout |
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507 | |
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508 | \begin_layout Standard |
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509 | Because grid is composed of domain and axis, all processing are taken grid |
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510 | via Domain and Axis. |
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511 | The next chapters supply the detail of these two sub components. |
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512 | |
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513 | \end_layout |
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514 | |
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515 | \end_body |
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516 | \end_document |
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