[669] | 1 | #LyX 2.1 created this file. For more info see http://www.lyx.org/ |
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| 2 | \lyxformat 474 |
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| 3 | \begin_document |
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| 4 | \begin_header |
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| 5 | \textclass book |
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| 6 | \use_default_options true |
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| 7 | \master ../../XIOS_user_guide.lyx |
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| 53 | \index Index |
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| 54 | \shortcut idx |
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| 56 | \end_index |
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| 57 | \secnumdepth 3 |
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| 58 | \tocdepth 3 |
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| 59 | \paragraph_separation indent |
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| 61 | \quotes_language english |
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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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[797] | 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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[669] | 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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[797] | 321 | <zoom_axis zoom_begin="1" zoom_n="3"/> |
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[669] | 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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[797] | 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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[669] | 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 |
---|
| 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 | |
---|
| 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 | |
---|
| 608 | \end_inset |
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| 609 | |
---|
| 610 | |
---|
| 611 | \end_layout |
---|
| 612 | |
---|
| 613 | \begin_layout Standard |
---|
| 614 | For local axis_A, the negative value of data_begin indicates that data is |
---|
| 615 | larger than local axis, the valid part of data needs extracted from the |
---|
| 616 | real data. |
---|
| 617 | If data_begin has a positive value, that means data size is smaller than |
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| 618 | local axis. |
---|
| 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 | |
---|
| 622 | \end_layout |
---|
| 623 | |
---|
| 624 | \begin_layout Standard |
---|
| 625 | Loal data can be defined with: |
---|
| 626 | \end_layout |
---|
| 627 | |
---|
| 628 | \begin_layout Standard |
---|
| 629 | \begin_inset listings |
---|
| 630 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
---|
| 631 | inline false |
---|
| 632 | status open |
---|
| 633 | |
---|
| 634 | \begin_layout Plain Layout |
---|
| 635 | |
---|
| 636 | CALL xios_set_axis_attr("axis_A",data_index=data) |
---|
| 637 | \end_layout |
---|
| 638 | |
---|
| 639 | \end_inset |
---|
| 640 | |
---|
| 641 | |
---|
| 642 | \end_layout |
---|
| 643 | |
---|
| 644 | \begin_layout Standard |
---|
| 645 | with |
---|
| 646 | \end_layout |
---|
| 647 | |
---|
| 648 | \begin_layout Itemize |
---|
| 649 | data = {-1,0,1,2,3} |
---|
| 650 | \end_layout |
---|
| 651 | |
---|
| 652 | \begin_layout Subsection |
---|
| 653 | Value |
---|
| 654 | \end_layout |
---|
| 655 | |
---|
| 656 | \begin_layout Standard |
---|
| 657 | Value of axis plays a same role as longitude and latitude of domain. |
---|
| 658 | As local data, it can be distributed among processes. |
---|
| 659 | \end_layout |
---|
| 660 | |
---|
| 661 | \begin_layout Standard |
---|
| 662 | \begin_inset listings |
---|
| 663 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
---|
| 664 | inline false |
---|
| 665 | status open |
---|
| 666 | |
---|
| 667 | \begin_layout Plain Layout |
---|
| 668 | |
---|
| 669 | CALL xios_set_axis_attr("axis_A", value=valueAxis) |
---|
| 670 | \end_layout |
---|
| 671 | |
---|
| 672 | \end_inset |
---|
| 673 | |
---|
| 674 | |
---|
| 675 | \end_layout |
---|
| 676 | |
---|
| 677 | \begin_layout Standard |
---|
| 678 | with |
---|
| 679 | \end_layout |
---|
| 680 | |
---|
| 681 | \begin_layout Itemize |
---|
| 682 | valueAxis = {30, 40, 50} |
---|
| 683 | \end_layout |
---|
| 684 | |
---|
| 685 | \begin_layout Standard |
---|
| 686 | Because there is a need of direction of an axis, then comes the attribute |
---|
| 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}}}" |
---|
| 693 | inline false |
---|
| 694 | status open |
---|
| 695 | |
---|
| 696 | \begin_layout Plain Layout |
---|
| 697 | |
---|
| 698 | CALL xios_set_axis_attr("axis_A", positive='up') |
---|
| 699 | \end_layout |
---|
| 700 | |
---|
| 701 | \end_inset |
---|
| 702 | |
---|
| 703 | |
---|
| 704 | \end_layout |
---|
| 705 | |
---|
| 706 | \begin_layout Standard |
---|
| 707 | All attributes of axis can be found in Reference Guide. |
---|
| 708 | \end_layout |
---|
| 709 | |
---|
| 710 | \begin_layout Standard |
---|
| 711 | |
---|
| 712 | \end_layout |
---|
| 713 | |
---|
| 714 | \end_body |
---|
| 715 | \end_document |
---|