[1084] | 1 | #LyX 2.2 created this file. For more info see http://www.lyx.org/ |
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| 2 | \lyxformat 508 |
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[669] | 3 | \begin_document |
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| 4 | \begin_header |
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[1084] | 5 | \save_transient_properties true |
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[669] | 7 | \textclass book |
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| 8 | \use_default_options true |
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| 9 | \master ../../XIOS_user_guide.lyx |
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| 11 | \language english |
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| 51 | \paperorientation portrait |
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| 55 | \index Index |
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| 56 | \shortcut idx |
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| 57 | \color #008000 |
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| 58 | \end_index |
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| 59 | \secnumdepth 3 |
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| 60 | \tocdepth 3 |
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| 61 | \paragraph_separation indent |
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| 62 | \paragraph_indentation default |
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| 63 | \quotes_language english |
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| 64 | \papercolumns 1 |
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| 65 | \papersides 1 |
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| 72 | \end_header |
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| 73 | |
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| 74 | \begin_body |
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| 75 | |
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| 76 | \begin_layout Chapter |
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| 77 | Axis |
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| 78 | \end_layout |
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| 79 | |
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| 80 | \begin_layout Standard |
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| 81 | Like Domain, Axis is a sub-component of Grid but is one dimension. |
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| 82 | In meteorological applications, axis represents a vertical line with different |
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| 83 | levels. |
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| 84 | \end_layout |
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| 85 | |
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| 86 | \begin_layout Section |
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| 87 | Working with configuration file |
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| 88 | \end_layout |
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| 89 | |
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| 90 | \begin_layout Standard |
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| 91 | The way to define an axis with configuration file is similar to define a |
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| 92 | domain. |
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| 93 | \end_layout |
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| 94 | |
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| 95 | \begin_layout Subsection |
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| 96 | Basic configuration |
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| 97 | \end_layout |
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| 98 | |
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| 99 | \begin_layout Standard |
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| 100 | Similar to domain, an axis is defined inside its definition part with the |
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| 101 | tag |
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| 102 | \series bold |
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| 103 | \color black |
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| 104 | axis_definition |
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| 105 | \series default |
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| 106 | \color inherit |
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| 107 | . |
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| 108 | |
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| 109 | \begin_inset listings |
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| 110 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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| 111 | inline false |
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| 112 | status open |
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| 113 | |
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| 114 | \begin_layout Plain Layout |
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| 115 | |
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| 116 | <axis_definition> |
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| 117 | \end_layout |
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| 118 | |
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| 119 | \begin_layout Plain Layout |
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| 120 | |
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| 121 | <axis id="axis_A" /> |
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| 122 | \end_layout |
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| 123 | |
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| 124 | \begin_layout Plain Layout |
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| 125 | |
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| 126 | <axis axis_ref="axis_A" /> |
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| 127 | \end_layout |
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| 128 | |
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| 129 | \begin_layout Plain Layout |
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| 130 | |
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| 131 | </axis_definition> |
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| 132 | \end_layout |
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| 133 | |
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| 134 | \end_inset |
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| 135 | |
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| 136 | |
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| 137 | \end_layout |
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| 138 | |
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| 139 | \begin_layout Standard |
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| 140 | The first one is to specify explicitly identification of an axis with an |
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| 141 | id. |
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| 142 | |
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| 143 | \end_layout |
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| 144 | |
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| 145 | \begin_layout Standard |
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| 146 | \begin_inset listings |
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| 147 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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| 148 | inline false |
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| 149 | status open |
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| 150 | |
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| 151 | \begin_layout Plain Layout |
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| 152 | |
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| 153 | <axis_definition> |
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| 154 | \end_layout |
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| 155 | |
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| 156 | \begin_layout Plain Layout |
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| 157 | |
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| 158 | <axis id="axis_A" /> |
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| 159 | \end_layout |
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| 160 | |
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| 161 | \begin_layout Plain Layout |
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| 162 | |
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| 163 | </axis_definition> |
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| 164 | \end_layout |
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| 165 | |
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| 166 | \end_inset |
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| 167 | |
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| 168 | |
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| 169 | \end_layout |
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| 170 | |
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| 171 | \begin_layout Standard |
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| 172 | In this way, with id, the axis can be processed, e.x modified its attributes, |
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| 173 | with Fortran interface; besides, it is only possible to reference to a |
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| 174 | axis whose id is explicitly defined. |
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| 175 | \end_layout |
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| 176 | |
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| 177 | \begin_layout Standard |
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| 178 | To make a reference to an axis, we use axis_ref |
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| 179 | \end_layout |
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| 180 | |
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| 181 | \begin_layout Standard |
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| 182 | \begin_inset listings |
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| 183 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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| 184 | inline false |
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| 185 | status open |
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| 186 | |
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| 187 | \begin_layout Plain Layout |
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| 188 | |
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| 189 | <axis_definition> |
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| 190 | \end_layout |
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| 191 | |
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| 192 | \begin_layout Plain Layout |
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| 193 | |
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| 194 | <axis axis_ref="axis_A" /> |
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| 195 | \end_layout |
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| 196 | |
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| 197 | \begin_layout Plain Layout |
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| 198 | |
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| 199 | </axis_definition> |
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| 200 | \end_layout |
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| 201 | |
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| 202 | \end_inset |
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| 203 | |
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| 204 | |
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| 205 | \end_layout |
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| 206 | |
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| 207 | \begin_layout Standard |
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| 208 | An axis defined by axis_ref will inherit all attributes of the referenced |
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| 209 | one, except its id attribute. |
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| 210 | If there is no id specified, an implicit one is assigned to this new axis. |
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| 211 | The axis with implicit id can only be used inside the scope where it is |
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| 212 | defined, it can not be referenced, nor be processed. |
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[1084] | 213 | It is useless to define an axis without id inside axis_definition. |
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[669] | 214 | |
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| 215 | \end_layout |
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| 216 | |
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| 217 | \begin_layout Standard |
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| 218 | To define a new axis inside a grid, we use the tag |
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| 219 | \series bold |
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| 220 | \color black |
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| 221 | axis. |
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| 222 | \end_layout |
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| 223 | |
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| 224 | \begin_layout Standard |
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| 225 | \begin_inset listings |
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| 226 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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| 227 | inline false |
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| 228 | status open |
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| 229 | |
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| 230 | \begin_layout Plain Layout |
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| 231 | |
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| 232 | <grid id="grid_A"> |
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| 233 | \end_layout |
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| 234 | |
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| 235 | \begin_layout Plain Layout |
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| 236 | |
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| 237 | <axis axis_ref="axis_A" /> |
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| 238 | \end_layout |
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| 239 | |
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| 240 | \begin_layout Plain Layout |
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| 241 | |
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| 242 | </grid> |
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| 243 | \end_layout |
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| 244 | |
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| 245 | \end_inset |
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| 246 | |
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| 247 | |
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| 248 | \end_layout |
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| 249 | |
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| 250 | \begin_layout Standard |
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| 251 | The xml lines above can be translated as: the grid_A composed of an axis_A |
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| 252 | that is defined somewhere else before. |
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| 253 | More precisely, the grid grid_A is constituted of a |
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| 254 | \begin_inset Quotes eld |
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| 255 | \end_inset |
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| 256 | |
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| 257 | unknown id |
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| 258 | \begin_inset Quotes erd |
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| 259 | \end_inset |
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| 260 | |
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| 261 | axis which has inherited all attributes (and their values) from axis A |
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| 262 | (name, long name, i_index, j_index, ... |
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| 263 | etc). |
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| 264 | \end_layout |
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| 265 | |
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| 266 | \begin_layout Subsection |
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| 267 | Advanced configuration |
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| 268 | \end_layout |
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| 269 | |
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| 270 | \begin_layout Standard |
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[1084] | 271 | Like domain, transformation which can be defined inside an axis. |
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[669] | 272 | All transformations on an axis have form *_axis. |
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[1084] | 273 | See Chapter |
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| 274 | \begin_inset CommandInset ref |
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| 275 | LatexCommand ref |
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| 276 | reference "chap:Transformation" |
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[669] | 277 | |
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| 278 | \end_inset |
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| 279 | |
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[1084] | 280 | for more details. |
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[669] | 281 | \end_layout |
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| 282 | |
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| 283 | \begin_layout Section |
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| 284 | Working with FORTRAN code |
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| 285 | \end_layout |
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| 286 | |
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| 287 | \begin_layout Standard |
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[1084] | 288 | Although axis is not as complex as domain, there are some mandatory attributes |
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[669] | 289 | to define. |
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| 290 | Different from precedent version, XIOS 2.0 supports distribution of data |
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| 291 | on a axis. |
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| 292 | The followings describe the essential parts of axis. |
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| 293 | Details of its attributes and operations can be found in XIOS reference |
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| 294 | guide. |
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| 295 | \end_layout |
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| 296 | |
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| 297 | \begin_layout Subsection |
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| 298 | Local axis index |
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| 299 | \end_layout |
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| 300 | |
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| 301 | \begin_layout Standard |
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| 302 | Axis is often used with domain, which is broken into several distributed |
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| 303 | pieces, to make a 3 dimension grid. |
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| 304 | However, there are cases in which data on axis are distributed among processes. |
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| 305 | Following we consider a simple case: a axis with global size 9 and its |
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| 306 | data are distributed evenly among 3 client processes, each of which has |
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| 307 | size 3. |
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| 308 | \end_layout |
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| 309 | |
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| 310 | \begin_layout Standard |
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| 311 | \begin_inset Float figure |
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| 312 | placement !tbph |
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| 313 | wide false |
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| 314 | sideways false |
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| 315 | status open |
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| 316 | |
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| 317 | \begin_layout Plain Layout |
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| 318 | \begin_inset Graphics |
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| 319 | filename ../images/Distributed_Axis.pdf |
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| 320 | lyxscale 50 |
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| 321 | scale 60 |
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| 322 | |
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| 323 | \end_inset |
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| 324 | |
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| 325 | |
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| 326 | \end_layout |
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| 327 | |
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| 328 | \begin_layout Plain Layout |
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| 329 | \begin_inset Caption Standard |
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| 330 | |
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| 331 | \begin_layout Plain Layout |
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| 332 | Global axis data |
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| 333 | \end_layout |
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| 334 | |
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| 335 | \end_inset |
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| 336 | |
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| 337 | |
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| 338 | \begin_inset CommandInset label |
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| 339 | LatexCommand label |
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| 340 | name "globalAxis" |
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| 341 | |
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| 342 | \end_inset |
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| 343 | |
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| 344 | |
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| 345 | \end_layout |
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| 346 | |
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| 347 | \end_inset |
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| 348 | |
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| 349 | |
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| 350 | \end_layout |
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| 351 | |
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| 352 | \begin_layout Standard |
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| 353 | The local axis can be described by the following way. |
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| 354 | \end_layout |
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| 355 | |
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| 356 | \begin_layout Standard |
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| 357 | Specify the the beginning and size of local axis with: |
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| 358 | \end_layout |
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| 359 | |
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| 360 | \begin_layout Itemize |
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| 361 | n_glo: global size of axis. |
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| 362 | |
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| 363 | \end_layout |
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| 364 | |
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| 365 | \begin_layout Itemize |
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| 366 | begin: global position where a local axis begin |
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| 367 | \end_layout |
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| 368 | |
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| 369 | \begin_layout Itemize |
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| 370 | n: local size of axis on each process |
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| 371 | \end_layout |
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| 372 | |
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| 373 | \begin_layout Standard |
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| 374 | For example, the local axis in the middle (the yellow one) can be specified |
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| 375 | with: |
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| 376 | \end_layout |
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| 377 | |
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| 378 | \begin_layout Standard |
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| 379 | \begin_inset listings |
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| 380 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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| 381 | inline false |
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| 382 | status open |
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| 383 | |
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| 384 | \begin_layout Plain Layout |
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| 385 | |
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| 386 | CALL xios_set_axis_attr("axis_A",n_glo=9, begin=3, n=3) |
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| 387 | \end_layout |
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| 388 | |
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| 389 | \end_inset |
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| 390 | |
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| 391 | |
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| 392 | \end_layout |
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| 393 | |
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| 394 | \begin_layout Subsection |
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| 395 | Local axis data |
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| 396 | \end_layout |
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| 397 | |
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| 398 | \begin_layout Standard |
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| 399 | Simpler than local domain data, data on axis is always on-dimension. |
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| 400 | Like local domain data, local axis data represent the data offset from |
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| 401 | local axis, and it can be defined in two ways. |
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| 402 | \end_layout |
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| 403 | |
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| 404 | \begin_layout Standard |
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[1084] | 405 | Specify the beginning and size of data on the local axis: |
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[669] | 406 | \end_layout |
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| 407 | |
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| 408 | \begin_layout Itemize |
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| 409 | data_begin: the local position of data on axis where data begins |
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| 410 | \end_layout |
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| 411 | |
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| 412 | \begin_layout Itemize |
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| 413 | data_n: size of data on each local axis |
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| 414 | \end_layout |
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| 415 | |
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| 416 | \begin_layout Standard |
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| 417 | Or specify data with its position in the local axis: |
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| 418 | \end_layout |
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| 419 | |
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| 420 | \begin_layout Itemize |
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| 421 | data_index: array of local position of data in the local axis. |
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| 422 | \end_layout |
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| 423 | |
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| 424 | \begin_layout Standard |
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[1084] | 425 | Although the valid data must be inside a local axis, it is not necessary |
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[669] | 426 | for data to have same size. |
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| 427 | In fact, data can have larger size than local axis. |
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| 428 | \end_layout |
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| 429 | |
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| 430 | \begin_layout Standard |
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| 431 | \begin_inset listings |
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| 432 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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| 433 | inline false |
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| 434 | status open |
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| 435 | |
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| 436 | \begin_layout Plain Layout |
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| 437 | |
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| 438 | CALL xios_set_axis_attr("axis_A", data_begin=-1, data_n=n+2) |
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| 439 | \end_layout |
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| 440 | |
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| 441 | \end_inset |
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| 442 | |
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| 443 | |
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| 444 | \end_layout |
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| 445 | |
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| 446 | \begin_layout Standard |
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| 447 | For local axis_A, the negative value of data_begin indicates that data is |
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| 448 | larger than local axis, the valid part of data needs extracted from the |
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| 449 | real data. |
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| 450 | If data_begin has a positive value, that means data size is smaller than |
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| 451 | local axis. |
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| 452 | The default value of data_begin is 0, which implies that local data fit |
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| 453 | into local axis properly. |
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| 454 | |
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| 455 | \end_layout |
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| 456 | |
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| 457 | \begin_layout Standard |
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[1084] | 458 | Local data can be defined with: |
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[669] | 459 | \end_layout |
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| 460 | |
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| 461 | \begin_layout Standard |
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| 462 | \begin_inset listings |
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| 463 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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| 464 | inline false |
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| 465 | status open |
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| 466 | |
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| 467 | \begin_layout Plain Layout |
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| 468 | |
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| 469 | CALL xios_set_axis_attr("axis_A",data_index=data) |
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| 470 | \end_layout |
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| 471 | |
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| 472 | \end_inset |
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| 473 | |
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| 474 | |
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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 | with |
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| 479 | \end_layout |
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| 480 | |
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| 481 | \begin_layout Itemize |
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| 482 | data = {-1,0,1,2,3} |
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| 483 | \end_layout |
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| 484 | |
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| 485 | \begin_layout Subsection |
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| 486 | Value |
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| 487 | \end_layout |
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| 488 | |
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| 489 | \begin_layout Standard |
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| 490 | Value of axis plays a same role as longitude and latitude of domain. |
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| 491 | As local data, it can be distributed among processes. |
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| 492 | \end_layout |
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| 493 | |
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| 494 | \begin_layout Standard |
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| 495 | \begin_inset listings |
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| 496 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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| 497 | inline false |
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| 498 | status open |
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| 499 | |
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| 500 | \begin_layout Plain Layout |
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| 501 | |
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| 502 | CALL xios_set_axis_attr("axis_A", value=valueAxis) |
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| 503 | \end_layout |
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| 504 | |
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| 505 | \end_inset |
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| 506 | |
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| 507 | |
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| 508 | \end_layout |
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| 509 | |
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| 510 | \begin_layout Standard |
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| 511 | with |
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| 512 | \end_layout |
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| 513 | |
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| 514 | \begin_layout Itemize |
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| 515 | valueAxis = {30, 40, 50} |
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| 516 | \end_layout |
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| 517 | |
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| 518 | \begin_layout Standard |
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| 519 | Because there is a need of direction of an axis, then comes the attribute |
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| 520 | positive |
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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 | \begin_inset listings |
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| 525 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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| 526 | inline false |
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| 527 | status open |
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| 528 | |
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| 529 | \begin_layout Plain Layout |
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| 530 | |
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| 531 | CALL xios_set_axis_attr("axis_A", positive='up') |
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| 532 | \end_layout |
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| 533 | |
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| 534 | \end_inset |
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| 535 | |
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| 536 | |
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| 537 | \end_layout |
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| 538 | |
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| 539 | \begin_layout Standard |
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| 540 | All attributes of axis can be found in Reference Guide. |
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| 541 | \end_layout |
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| 542 | |
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| 543 | \begin_layout Standard |
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| 544 | |
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| 545 | \end_layout |
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| 546 | |
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| 547 | \end_body |
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| 548 | \end_document |
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