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3 | \begin_document |
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4 | \begin_header |
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7 | \master ../../XIOS_user_guide.lyx |
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70 | \end_header |
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71 | |
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72 | \begin_body |
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73 | |
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74 | \begin_layout Chapter |
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75 | Axis |
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76 | \end_layout |
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77 | |
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78 | \begin_layout Standard |
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79 | Like Domain, Axis is a sub-component of Grid but is one dimension. |
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80 | In meteorological applications, axis represents a vertical line with different |
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81 | levels. |
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82 | \end_layout |
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83 | |
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84 | \begin_layout Section |
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85 | Working with configuration file |
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86 | \end_layout |
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87 | |
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88 | \begin_layout Standard |
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89 | The way to define an axis with configuration file is similar to define a |
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90 | domain. |
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91 | \end_layout |
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92 | |
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93 | \begin_layout Subsection |
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94 | Basic configuration |
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95 | \end_layout |
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96 | |
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97 | \begin_layout Standard |
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98 | Similar to domain, an axis is defined inside its definition part with the |
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99 | tag |
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100 | \series bold |
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101 | \color black |
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102 | axis_definition |
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103 | \series default |
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104 | \color inherit |
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105 | . |
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106 | |
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107 | \begin_inset listings |
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108 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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109 | inline false |
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110 | status open |
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111 | |
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112 | \begin_layout Plain Layout |
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113 | |
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114 | <axis_definition> |
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115 | \end_layout |
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116 | |
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117 | \begin_layout Plain Layout |
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118 | |
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119 | <axis id="axis_A" /> |
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120 | \end_layout |
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121 | |
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122 | \begin_layout Plain Layout |
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123 | |
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124 | <axis axis_ref="axis_A" /> |
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125 | \end_layout |
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126 | |
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127 | \begin_layout Plain Layout |
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128 | |
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129 | </axis_definition> |
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130 | \end_layout |
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131 | |
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132 | \end_inset |
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133 | |
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134 | |
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135 | \end_layout |
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136 | |
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137 | \begin_layout Standard |
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138 | The first one is to specify explicitly identification of an axis with an |
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139 | id. |
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140 | |
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141 | \end_layout |
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142 | |
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143 | \begin_layout Standard |
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144 | \begin_inset listings |
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145 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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146 | inline false |
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147 | status open |
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148 | |
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149 | \begin_layout Plain Layout |
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150 | |
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151 | <axis_definition> |
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152 | \end_layout |
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153 | |
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154 | \begin_layout Plain Layout |
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155 | |
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156 | <axis id="axis_A" /> |
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157 | \end_layout |
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158 | |
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159 | \begin_layout Plain Layout |
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160 | |
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161 | </axis_definition> |
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162 | \end_layout |
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163 | |
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164 | \end_inset |
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165 | |
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166 | |
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167 | \end_layout |
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168 | |
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169 | \begin_layout Standard |
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170 | In this way, with id, the axis can be processed, e.x modified its attributes, |
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171 | with Fortran interface; besides, it is only possible to reference to a |
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172 | axis whose id is explicitly defined. |
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173 | \end_layout |
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174 | |
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175 | \begin_layout Standard |
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176 | To make a reference to an axis, we use axis_ref |
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177 | \end_layout |
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178 | |
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179 | \begin_layout Standard |
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180 | \begin_inset listings |
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181 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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182 | inline false |
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183 | status open |
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184 | |
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185 | \begin_layout Plain Layout |
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186 | |
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187 | <axis_definition> |
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188 | \end_layout |
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189 | |
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190 | \begin_layout Plain Layout |
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191 | |
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192 | <axis axis_ref="axis_A" /> |
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193 | \end_layout |
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194 | |
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195 | \begin_layout Plain Layout |
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196 | |
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197 | </axis_definition> |
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198 | \end_layout |
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199 | |
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200 | \end_inset |
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201 | |
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202 | |
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203 | \end_layout |
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204 | |
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205 | \begin_layout Standard |
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206 | An axis defined by axis_ref will inherit all attributes of the referenced |
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207 | one, except its id attribute. |
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208 | If there is no id specified, an implicit one is assigned to this new axis. |
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209 | The axis with implicit id can only be used inside the scope where it is |
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210 | defined, it can not be referenced, nor be processed. |
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211 | It is rare to define an axis without id inside axis_definition. |
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212 | |
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213 | \end_layout |
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214 | |
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215 | \begin_layout Standard |
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216 | To define a new axis inside a grid, we use the tag |
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217 | \series bold |
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218 | \color black |
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219 | axis. |
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220 | \end_layout |
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221 | |
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222 | \begin_layout Standard |
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223 | \begin_inset listings |
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224 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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225 | inline false |
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226 | status open |
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227 | |
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228 | \begin_layout Plain Layout |
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229 | |
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230 | <grid id="grid_A"> |
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231 | \end_layout |
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232 | |
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233 | \begin_layout Plain Layout |
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234 | |
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235 | <axis axis_ref="axis_A" /> |
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236 | \end_layout |
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237 | |
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238 | \begin_layout Plain Layout |
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239 | |
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240 | </grid> |
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241 | \end_layout |
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242 | |
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243 | \end_inset |
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244 | |
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245 | |
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246 | \end_layout |
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247 | |
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248 | \begin_layout Standard |
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249 | The xml lines above can be translated as: the grid_A composed of an axis_A |
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250 | that is defined somewhere else before. |
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251 | More precisely, the grid grid_A is constituted of a |
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252 | \begin_inset Quotes eld |
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253 | \end_inset |
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254 | |
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255 | unknown id |
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256 | \begin_inset Quotes erd |
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257 | \end_inset |
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258 | |
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259 | axis which has inherited all attributes (and their values) from axis A |
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260 | (name, long name, i_index, j_index, ... |
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261 | etc). |
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262 | \end_layout |
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263 | |
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264 | \begin_layout Subsection |
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265 | Advanced configuration |
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266 | \end_layout |
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267 | |
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268 | \begin_layout Standard |
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269 | Like domain, there are several transformation which can be defined with |
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270 | configuration file. |
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271 | All transformations on an axis have form *_axis. |
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272 | |
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273 | \end_layout |
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274 | |
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275 | \begin_layout Standard |
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276 | Till now, XIOS supports the following transformation on axis: |
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277 | \end_layout |
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278 | |
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279 | \begin_layout Itemize |
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280 | zoom_axis: Like zoom functionality in XIOS 1.0, the destination grid is the |
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281 | zoomed region of the source grid. |
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282 | \end_layout |
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283 | |
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284 | \begin_layout Itemize |
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285 | interpolation_axis: Implement interpolation from an axis to one another. |
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286 | For now, only polynominal interpolation is available. |
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287 | \end_layout |
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288 | |
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289 | \begin_layout Itemize |
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290 | inverse_axis: Inverse an axis |
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291 | \end_layout |
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292 | |
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293 | \begin_layout Standard |
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294 | It is not difficult to define a transformation: Include type of transformation |
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295 | inside axis definition, as the following |
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296 | \end_layout |
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297 | |
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298 | \begin_layout Standard |
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299 | \begin_inset listings |
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300 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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301 | inline false |
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302 | status open |
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303 | |
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304 | \begin_layout Plain Layout |
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305 | |
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306 | <axis_definition> |
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307 | \end_layout |
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308 | |
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309 | \begin_layout Plain Layout |
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310 | |
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311 | <axis id="axis_A" /> |
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312 | \end_layout |
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313 | |
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314 | \begin_layout Plain Layout |
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315 | |
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316 | <axis id="axis_A_zoom" axis_ref="axis_A"> |
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317 | \end_layout |
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318 | |
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319 | \begin_layout Plain Layout |
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320 | |
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321 | <zoom_axis zoom_begin="1" zoom_n="3"/> |
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322 | \end_layout |
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323 | |
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324 | \begin_layout Plain Layout |
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325 | |
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326 | </axis> |
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327 | \end_layout |
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328 | |
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329 | \begin_layout Plain Layout |
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330 | |
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331 | </axis_definition> |
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332 | \end_layout |
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333 | |
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334 | \end_inset |
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335 | |
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336 | |
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337 | \end_layout |
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338 | |
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339 | \begin_layout Standard |
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340 | The concrete example is translated as: the axis named axis_A_zoom is transformed |
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341 | from axis name axis_A with a zoom activity. |
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342 | The detailed attributes of zoom_axis can be found in reference document, |
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343 | but simply it contains the begining and size of zoomed region. |
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344 | \end_layout |
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345 | |
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346 | \begin_layout Standard |
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347 | One remark is the transformed axis SHOULD have an id, in this case, it's |
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348 | axis_A_zoom. |
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349 | As mentioned before, a no-id axis or any no-id component of XIOS can only |
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350 | be used inside its definition scope. |
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351 | \end_layout |
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352 | |
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353 | \begin_layout Standard |
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354 | To make use of transformation, the grid must contain axis which references |
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355 | to transformed ones. |
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356 | |
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357 | \end_layout |
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358 | |
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359 | \begin_layout Standard |
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360 | \begin_inset listings |
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361 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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362 | inline false |
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363 | status open |
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364 | |
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365 | \begin_layout Plain Layout |
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366 | |
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367 | <grid id="grid_A"> |
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368 | \end_layout |
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369 | |
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370 | \begin_layout Plain Layout |
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371 | |
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372 | <axis axis_ref="axis_A" /> |
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373 | \end_layout |
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374 | |
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375 | \begin_layout Plain Layout |
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376 | |
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377 | </grid> |
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378 | \end_layout |
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379 | |
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380 | \begin_layout Plain Layout |
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381 | |
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382 | <grid id="grid_A_zoom"> |
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383 | \end_layout |
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384 | |
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385 | \begin_layout Plain Layout |
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386 | |
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387 | <axis axis_ref="axis_A_zoom" /> |
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388 | \end_layout |
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389 | |
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390 | \begin_layout Plain Layout |
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391 | |
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392 | </grid> |
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393 | \end_layout |
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394 | |
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395 | \end_inset |
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396 | |
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397 | |
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398 | \end_layout |
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399 | |
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400 | \begin_layout Standard |
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401 | On defining this way, we tell XIOS to establish a connection between two |
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402 | grids by a transformation (zoom) with: grid source - grid_A, grid destination |
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403 | - grid_A_zoom. |
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404 | \end_layout |
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405 | |
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406 | \begin_layout Standard |
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407 | As mentioned in Grid Chapter, in order to use transformed grid, just reference |
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408 | to it in field_definition |
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409 | \end_layout |
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410 | |
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411 | \begin_layout Standard |
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412 | \begin_inset listings |
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413 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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414 | inline false |
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415 | status open |
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416 | |
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417 | \begin_layout Plain Layout |
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418 | |
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419 | <field_definition level="1" enabled=".TRUE." default_value="9.96921e+36"> |
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420 | \end_layout |
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421 | |
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422 | \begin_layout Plain Layout |
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423 | |
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424 | <field id="field_A" operation="average" freq_op="3600s" grid_ref="grid_A" |
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425 | /> |
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426 | \end_layout |
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427 | |
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428 | \begin_layout Plain Layout |
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429 | |
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430 | <field id="field_A_zoom" operation="average" freq_op="3600s" grid_ref="grid_A |
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431 | _zoom" /> |
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432 | \end_layout |
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433 | |
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434 | \begin_layout Plain Layout |
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435 | |
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436 | </field_definition> |
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437 | \end_layout |
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438 | |
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439 | \end_inset |
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440 | |
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441 | |
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442 | \end_layout |
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443 | |
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444 | \begin_layout Standard |
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445 | Although xml is helpful to define several configurations, it can not be |
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446 | used to customize attributes of axis. |
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447 | So it's the turn of Fortran interface. |
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448 | \end_layout |
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449 | |
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450 | \begin_layout Section |
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451 | Working with FORTRAN code |
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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 | Although axis is not as complexe as domain, there are some mandatory attributes |
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456 | to define. |
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457 | Different from precedent version, XIOS 2.0 supports distribution of data |
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458 | on a axis. |
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459 | The followings describe the essential parts of axis. |
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460 | Details of its attributes and operations can be found in XIOS reference |
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461 | guide. |
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462 | \end_layout |
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463 | |
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464 | \begin_layout Subsection |
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465 | Local axis index |
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466 | \end_layout |
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467 | |
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468 | \begin_layout Standard |
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469 | Axis is often used with domain, which is broken into several distributed |
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470 | pieces, to make a 3 dimension grid. |
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471 | However, there are cases in which data on axis are distributed among processes. |
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472 | Following we consider a simple case: a axis with global size 9 and its |
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473 | data are distributed evenly among 3 client processes, each of which has |
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474 | size 3. |
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475 | \end_layout |
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476 | |
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477 | \begin_layout Standard |
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478 | \begin_inset Float figure |
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479 | placement !tbph |
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480 | wide false |
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481 | sideways false |
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482 | status open |
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483 | |
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484 | \begin_layout Plain Layout |
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485 | \begin_inset Graphics |
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486 | filename ../images/Distributed_Axis.pdf |
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487 | lyxscale 50 |
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488 | scale 60 |
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489 | |
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490 | \end_inset |
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491 | |
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492 | |
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493 | \end_layout |
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494 | |
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495 | \begin_layout Plain Layout |
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496 | \begin_inset Caption Standard |
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497 | |
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498 | \begin_layout Plain Layout |
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499 | Global axis data |
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500 | \end_layout |
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501 | |
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502 | \end_inset |
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503 | |
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504 | |
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505 | \begin_inset CommandInset label |
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506 | LatexCommand label |
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507 | name "globalAxis" |
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508 | |
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509 | \end_inset |
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510 | |
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511 | |
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512 | \end_layout |
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513 | |
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514 | \end_inset |
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515 | |
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516 | |
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517 | \end_layout |
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518 | |
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519 | \begin_layout Standard |
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520 | The local axis can be described by the following way. |
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521 | \end_layout |
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522 | |
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523 | \begin_layout Standard |
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524 | Specify the the beginning and size of local axis with: |
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525 | \end_layout |
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526 | |
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527 | \begin_layout Itemize |
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528 | n_glo: global size of axis. |
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529 | |
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530 | \end_layout |
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531 | |
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532 | \begin_layout Itemize |
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533 | begin: global position where a local axis begin |
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534 | \end_layout |
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535 | |
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536 | \begin_layout Itemize |
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537 | n: local size of axis on each process |
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538 | \end_layout |
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539 | |
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540 | \begin_layout Standard |
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541 | For example, the local axis in the middle (the yellow one) can be specified |
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542 | with: |
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543 | \end_layout |
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544 | |
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545 | \begin_layout Standard |
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546 | \begin_inset listings |
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547 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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548 | inline false |
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549 | status open |
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550 | |
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551 | \begin_layout Plain Layout |
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552 | |
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553 | CALL xios_set_axis_attr("axis_A",n_glo=9, begin=3, n=3) |
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554 | \end_layout |
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555 | |
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556 | \end_inset |
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557 | |
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558 | |
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559 | \end_layout |
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560 | |
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561 | \begin_layout Subsection |
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562 | Local axis data |
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563 | \end_layout |
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564 | |
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565 | \begin_layout Standard |
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566 | Simpler than local domain data, data on axis is always on-dimension. |
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567 | Like local domain data, local axis data represent the data offset from |
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568 | local axis, and it can be defined in two ways. |
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569 | \end_layout |
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570 | |
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571 | \begin_layout Standard |
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572 | Specify the begining and size of data on the local axis: |
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573 | \end_layout |
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574 | |
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575 | \begin_layout Itemize |
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576 | data_begin: the local position of data on axis where data begins |
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577 | \end_layout |
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578 | |
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579 | \begin_layout Itemize |
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580 | data_n: size of data on each local axis |
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581 | \end_layout |
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582 | |
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583 | \begin_layout Standard |
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584 | Or specify data with its position in the local axis: |
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585 | \end_layout |
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586 | |
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587 | \begin_layout Itemize |
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588 | data_index: array of local position of data in the local axis. |
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589 | \end_layout |
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590 | |
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591 | \begin_layout Standard |
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592 | Although the valid data must be inside a local axis, it is not neccessary |
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593 | for data to have same size. |
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594 | In fact, data can have larger size than local axis. |
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595 | \end_layout |
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596 | |
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597 | \begin_layout Standard |
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598 | \begin_inset listings |
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599 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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600 | inline false |
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601 | status open |
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602 | |
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603 | \begin_layout Plain Layout |
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604 | |
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605 | CALL xios_set_axis_attr("axis_A", data_begin=-1, data_n=n+2) |
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606 | \end_layout |
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607 | |
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608 | \end_inset |
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609 | |
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610 | |
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611 | \end_layout |
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612 | |
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613 | \begin_layout Standard |
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614 | For local axis_A, the negative value of data_begin indicates that data is |
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615 | larger than local axis, the valid part of data needs extracted from the |
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616 | real data. |
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617 | If data_begin has a positive value, that means data size is smaller than |
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618 | local axis. |
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619 | The default value of data_begin is 0, which implies that local data fit |
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620 | into local axis properly. |
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621 | |
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622 | \end_layout |
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623 | |
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624 | \begin_layout Standard |
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625 | Loal data can be defined with: |
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626 | \end_layout |
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627 | |
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628 | \begin_layout Standard |
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629 | \begin_inset listings |
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630 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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631 | inline false |
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632 | status open |
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633 | |
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634 | \begin_layout Plain Layout |
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635 | |
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636 | CALL xios_set_axis_attr("axis_A",data_index=data) |
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637 | \end_layout |
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638 | |
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639 | \end_inset |
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640 | |
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641 | |
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642 | \end_layout |
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643 | |
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644 | \begin_layout Standard |
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645 | with |
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646 | \end_layout |
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647 | |
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648 | \begin_layout Itemize |
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649 | data = {-1,0,1,2,3} |
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650 | \end_layout |
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651 | |
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652 | \begin_layout Subsection |
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653 | Value |
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654 | \end_layout |
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655 | |
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656 | \begin_layout Standard |
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657 | Value of axis plays a same role as longitude and latitude of domain. |
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658 | As local data, it can be distributed among processes. |
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659 | \end_layout |
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660 | |
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661 | \begin_layout Standard |
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662 | \begin_inset listings |
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663 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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664 | inline false |
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665 | status open |
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666 | |
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667 | \begin_layout Plain Layout |
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668 | |
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669 | CALL xios_set_axis_attr("axis_A", value=valueAxis) |
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670 | \end_layout |
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671 | |
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672 | \end_inset |
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673 | |
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674 | |
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675 | \end_layout |
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676 | |
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677 | \begin_layout Standard |
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678 | with |
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679 | \end_layout |
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680 | |
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681 | \begin_layout Itemize |
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682 | valueAxis = {30, 40, 50} |
---|
683 | \end_layout |
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684 | |
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685 | \begin_layout Standard |
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686 | Because there is a need of direction of an axis, then comes the attribute |
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687 | positive |
---|
688 | \end_layout |
---|
689 | |
---|
690 | \begin_layout Standard |
---|
691 | \begin_inset listings |
---|
692 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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693 | inline false |
---|
694 | status open |
---|
695 | |
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696 | \begin_layout Plain Layout |
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697 | |
---|
698 | CALL xios_set_axis_attr("axis_A", positive='up') |
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699 | \end_layout |
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700 | |
---|
701 | \end_inset |
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702 | |
---|
703 | |
---|
704 | \end_layout |
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705 | |
---|
706 | \begin_layout Standard |
---|
707 | All attributes of axis can be found in Reference Guide. |
---|
708 | \end_layout |
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709 | |
---|
710 | \begin_layout Standard |
---|
711 | |
---|
712 | \end_layout |
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713 | |
---|
714 | \end_body |
---|
715 | \end_document |
---|