[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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| 9 | \language english |
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| 53 | \index Index |
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| 54 | \shortcut idx |
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| 55 | \color #008000 |
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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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| 60 | \paragraph_indentation default |
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| 61 | \quotes_language english |
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| 63 | \papersides 1 |
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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 | Grid |
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| 76 | \end_layout |
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| 77 | |
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| 78 | \begin_layout Section |
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| 79 | Overview |
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| 80 | \end_layout |
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| 81 | |
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| 82 | \begin_layout Standard |
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| 83 | Grid plays an important role in XIOS. |
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| 84 | Same as Field, Grid is one of the basic elements in XIOS, which should |
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| 85 | be well defined, not only in the configuration file but also in the FORTRAN |
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| 86 | code. |
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| 87 | Because, until now, XIOS has mainly served for writing NetCDF data format, |
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| 88 | most of its components are inspired from NetCDF Data Model, and Grid is |
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| 89 | not an exception. |
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| 90 | Grid is a concept describing dimensions that contain the axes of the data |
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| 91 | arrays. |
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| 92 | Moreover, Grid always consists of an unlimited dimension whose length can |
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| 93 | be expanded at any time. |
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| 94 | Other dimensions can be described with Domain and Axis. |
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| 95 | The followings describe how to make use of Grid in XIOS. |
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| 96 | Details of its attributes and operations can be found in XIOS reference |
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| 97 | guide. |
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| 98 | \end_layout |
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| 99 | |
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| 100 | \begin_layout Section |
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| 101 | Working with configuration file |
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| 102 | \end_layout |
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| 103 | |
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| 104 | \begin_layout Standard |
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| 105 | As mentioned above, a grid contains the axes of the data arrays, which are |
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| 106 | characterized by Domain and/or Axis. |
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| 107 | A domain is composed of a 2-dimension array, meanwhile an axis is, as its |
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| 108 | name, an 1-dimension array. |
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| 109 | |
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| 110 | \end_layout |
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| 111 | |
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| 112 | \begin_layout Standard |
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| 113 | Like other components of XIOS, a grid is defined inside its definition part |
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| 114 | with the tag |
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| 115 | \series bold |
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| 116 | \color black |
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| 117 | grid_definition |
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| 118 | \series default |
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| 119 | \color inherit |
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| 120 | |
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| 121 | \begin_inset listings |
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| 122 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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| 123 | inline false |
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| 124 | status collapsed |
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| 125 | |
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| 126 | \begin_layout Plain Layout |
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| 127 | |
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| 128 | <grid_definition> |
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| 129 | \end_layout |
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| 130 | |
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| 131 | \begin_layout Plain Layout |
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| 132 | |
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| 133 | <grid_group id="gridGroup"> |
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| 134 | \end_layout |
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| 135 | |
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| 136 | \begin_layout Plain Layout |
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| 137 | |
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| 138 | <grid id="grid_A"> |
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| 139 | \end_layout |
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| 140 | |
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| 141 | \begin_layout Plain Layout |
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| 142 | |
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| 143 | <domain domain_ref="domain_A" /> |
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| 144 | \end_layout |
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| 145 | |
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| 146 | \begin_layout Plain Layout |
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| 147 | |
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| 148 | <axis axis_ref="axis_C" /> |
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| 149 | \end_layout |
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| 150 | |
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| 151 | \begin_layout Plain Layout |
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| 152 | |
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| 153 | </grid> |
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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 | <grid id="grid_Axis"> |
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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 axis_ref="axis_D" /> |
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| 164 | \end_layout |
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| 165 | |
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| 166 | \begin_layout Plain Layout |
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| 167 | |
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| 168 | </grid> |
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| 169 | \end_layout |
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| 170 | |
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| 171 | \begin_layout Plain Layout |
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| 172 | |
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| 173 | <grid id="grid_All_Axis"> |
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| 174 | \end_layout |
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| 175 | |
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| 176 | \begin_layout Plain Layout |
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| 177 | |
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| 178 | <axis axis_ref="axis_A" /> |
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| 179 | \end_layout |
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| 180 | |
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| 181 | \begin_layout Plain Layout |
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| 182 | |
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| 183 | <axis axis_ref="axis_B" /> |
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| 184 | \end_layout |
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| 185 | |
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| 186 | \begin_layout Plain Layout |
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| 187 | |
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| 188 | <axis axis_ref="axis_C" /> |
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| 189 | \end_layout |
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| 190 | |
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| 191 | \begin_layout Plain Layout |
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| 192 | |
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| 193 | </grid> |
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| 194 | \end_layout |
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| 195 | |
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| 196 | \begin_layout Plain Layout |
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| 197 | |
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| 198 | </grid_group> |
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| 199 | \end_layout |
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| 200 | |
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| 201 | \begin_layout Plain Layout |
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| 202 | |
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| 203 | </grid_definition> |
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| 204 | \end_layout |
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| 205 | |
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| 206 | \end_inset |
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| 207 | |
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| 208 | |
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| 209 | \end_layout |
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| 210 | |
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| 211 | \begin_layout Standard |
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| 212 | As XIOS supports netCDF-4/HDF5, it allows user to gather several grids into |
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| 213 | groups to better organize data. |
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| 214 | Very often, grids are grouped, basing on the dimensions that they describe. |
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| 215 | However, there is not a limit for user to group out the grids. |
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| 216 | The more important thing than grid_group is grid. |
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| 217 | A grid is defined with the tag |
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| 218 | \series bold |
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| 219 | \color black |
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| 220 | grid. |
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| 221 | |
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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 | While it is not crucial for a grid group not to have an identification specified |
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| 226 | by attribute id, a grid must be assigned an id to become useful. |
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| 227 | Unlike grid group is a way of hierarchically organizing related grid only, |
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| 228 | a grid itself is referenced by fields with its id. |
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| 229 | Without the id, a grid can not be made used of by a field. |
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| 230 | Id is a string of anything but there is one thing to remember: id of a |
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| 231 | grid as well as id of any component in XIOS are |
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| 232 | \shape italic |
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| 233 | \color black |
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| 234 | unique |
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| 235 | \shape default |
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| 236 | \color inherit |
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| 237 | among this kind of components. |
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| 238 | It is not allowed to have two grids with a same id, but it is permitted |
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| 239 | a grid and, for example, a domain to share a same one. |
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| 240 | |
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| 241 | \end_layout |
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| 242 | |
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| 243 | \begin_layout Standard |
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| 244 | A grid is defined by domain(s) and axis. |
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| 245 | A domain represents two-dimension data while an axis serves as one-dimension |
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| 246 | data. |
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| 247 | They are defined inside the grid definition. |
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| 248 | One of the convenient and effective way to reuse the definitions in XIOS |
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| 249 | is to take advantage of attribute *_ref. |
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| 250 | On using *_ref, the referencing component has all attributes from its reference |
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| 251 | d one. |
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| 252 | As the example below, grid with id |
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| 253 | \begin_inset Quotes eld |
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| 254 | \end_inset |
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| 255 | |
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| 256 | grid_A |
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| 257 | \begin_inset Quotes erd |
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| 258 | \end_inset |
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| 259 | |
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| 260 | (from now one, called grid_A), is composed of one domain whose attributes |
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| 261 | derived directly from another one-domain_A, and one axis whose attributes |
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| 262 | are taken from axis axis_C, which are defined previously. |
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| 263 | \end_layout |
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| 264 | |
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| 265 | \begin_layout Standard |
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| 266 | \begin_inset listings |
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| 267 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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| 268 | inline false |
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| 269 | status open |
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| 270 | |
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| 271 | \begin_layout Plain Layout |
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| 272 | |
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| 273 | <domain id="domain_A /> |
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| 274 | \end_layout |
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| 275 | |
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| 276 | \begin_layout Plain Layout |
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| 277 | |
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| 278 | <axis id="axis_A" /> |
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| 279 | \end_layout |
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| 280 | |
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| 281 | \begin_layout Plain Layout |
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| 282 | |
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| 283 | \end_layout |
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| 284 | |
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| 285 | \begin_layout Plain Layout |
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| 286 | |
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| 287 | <grid id="grid_A"> |
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| 288 | \end_layout |
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| 289 | |
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| 290 | \begin_layout Plain Layout |
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| 291 | |
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| 292 | <domain domain_ref="domain_A" /> |
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| 293 | \end_layout |
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| 294 | |
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| 295 | \begin_layout Plain Layout |
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| 296 | |
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| 297 | <axis axis_ref="axis_C" /> |
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| 298 | \end_layout |
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| 299 | |
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| 300 | \begin_layout Plain Layout |
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| 301 | |
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| 302 | </grid> |
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| 303 | \end_layout |
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| 304 | |
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| 305 | \end_inset |
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| 306 | |
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| 307 | |
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| 308 | \end_layout |
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| 309 | |
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| 310 | \begin_layout Standard |
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| 311 | The *_ref can only used to reference to a already defined element (e.g domain, |
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| 312 | axis, grid, etc). |
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| 313 | If these *_ref have not been defined yet, there will be a runtime error. |
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| 314 | \end_layout |
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| 315 | |
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| 316 | \begin_layout Standard |
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| 317 | Details about domain and axis can be found in other sections but there is |
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| 318 | one thing to bear in mind: A domain represents two-dimension data and it |
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| 319 | also contains several special information: longitude, latitude, bound, |
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| 320 | etc. |
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| 321 | For the meteorological mind, domain indicates a surface with latitude and |
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| 322 | longitude, whereas axis represents a vertical level. |
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| 323 | |
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| 324 | \end_layout |
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| 325 | |
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| 326 | \begin_layout Standard |
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| 327 | In general cases, there is only a need of writing some multidimensional |
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| 328 | data to a netCDF without any specific information, then comes the following |
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| 329 | definition of grid. |
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| 330 | \end_layout |
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| 331 | |
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| 332 | \begin_layout Standard |
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| 333 | \begin_inset listings |
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| 335 | inline false |
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| 336 | status open |
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| 337 | |
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| 338 | \begin_layout Plain Layout |
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| 339 | |
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| 340 | <grid id="grid_All_Axis"> |
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| 341 | \end_layout |
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| 342 | |
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| 343 | \begin_layout Plain Layout |
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| 344 | |
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| 345 | <axis axis_ref="axis_A" /> |
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| 346 | \end_layout |
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| 347 | |
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| 348 | \begin_layout Plain Layout |
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| 349 | |
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| 350 | <axis axis_ref="axis_B" /> |
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| 351 | \end_layout |
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| 352 | |
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| 353 | \begin_layout Plain Layout |
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| 354 | |
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| 355 | <axis axis_ref="axis_C" /> |
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| 356 | \end_layout |
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| 357 | |
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| 358 | \begin_layout Plain Layout |
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| 359 | |
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| 360 | </grid> |
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| 361 | \end_layout |
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| 362 | |
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| 363 | \end_inset |
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| 364 | |
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| 365 | |
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| 366 | \end_layout |
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| 367 | |
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| 368 | \begin_layout Standard |
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| 369 | The grid_All_Axis is similar to grid_A, but with three dimensions defined |
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| 370 | by 3 axis that can be described in any way on demand of user. |
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| 371 | For example, the axis_A and the axis_B can have corresponding name latitude |
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| 372 | and longitude to characterize a two-dimension surface with latitude and |
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| 373 | longitude. |
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| 374 | \end_layout |
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| 375 | |
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| 376 | \begin_layout Standard |
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| 377 | Very often, one dimensional data needs writing to netCDF, it can be easily |
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| 378 | done with the following XML code |
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| 379 | \end_layout |
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| 380 | |
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| 381 | \begin_layout Standard |
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| 382 | \begin_inset listings |
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| 383 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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| 384 | inline false |
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| 385 | status open |
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| 386 | |
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| 387 | \begin_layout Plain Layout |
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| 388 | |
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| 389 | <grid id="grid_Axis"> |
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| 390 | \end_layout |
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| 391 | |
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| 392 | \begin_layout Plain Layout |
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| 393 | |
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| 394 | <axis axis_ref="axis_D" /> |
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| 395 | \end_layout |
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| 396 | |
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| 397 | \begin_layout Plain Layout |
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| 398 | |
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| 399 | </grid> |
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| 400 | \end_layout |
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| 401 | |
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| 402 | \end_inset |
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| 403 | |
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| 404 | |
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| 405 | \end_layout |
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| 406 | |
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| 407 | \begin_layout Standard |
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| 408 | As it is discussed more details in the next section, but remember that even |
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| 409 | the non-distributed one dimensional data can be well processed by XIOS. |
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| 410 | |
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| 411 | \end_layout |
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| 412 | |
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| 413 | \begin_layout Standard |
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| 414 | As mentioned above, grid includes by default one unlimited dimension which |
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| 415 | is often used as time step axis. |
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| 416 | In order to write only time step to netCDF, XIOS provides a special way |
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| 417 | to do: empty grid - a grid without any domain or axis. |
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| 418 | \end_layout |
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| 419 | |
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| 420 | \begin_layout Standard |
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| 421 | \begin_inset listings |
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| 422 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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| 423 | inline false |
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| 424 | status open |
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| 425 | |
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| 426 | \begin_layout Plain Layout |
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| 427 | |
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| 428 | <grid id="grid_TimeStep"> |
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| 429 | \end_layout |
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| 430 | |
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| 431 | \begin_layout Plain Layout |
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| 432 | |
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| 433 | </grid> |
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| 434 | \end_layout |
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| 435 | |
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| 436 | \end_inset |
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| 437 | |
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| 438 | |
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| 439 | \end_layout |
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| 440 | |
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| 441 | \begin_layout Standard |
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| 442 | âThe order of domain and/or in grid definition decides order of data written |
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| 443 | to netCDF: data on domain or axis appearing firstly in grid definition |
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| 444 | will vary the most. |
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| 445 | For example, on using ncdump command on netCDF which contains data written |
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| 446 | on the grid_A . |
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| 447 | \end_layout |
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| 448 | |
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| 449 | \begin_layout Standard |
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| 450 | \begin_inset listings |
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| 451 | lstparams "language=XML,breaklines=true,tabsize=2,frame=tb,postbreak={\raisebox{0ex}[0ex][0ex]{\ensuremath{\rcurvearrowse\space}}}" |
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| 452 | inline false |
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| 453 | status open |
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| 454 | |
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| 455 | \begin_layout Plain Layout |
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| 456 | |
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| 457 | float field_A(time_counter, axis_A, y, x) ; |
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| 458 | \end_layout |
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| 459 | |
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| 460 | \begin_layout Plain Layout |
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| 461 | |
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| 462 | field_A:online_operation = "average" ; |
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| 463 | \end_layout |
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| 464 | |
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| 465 | \begin_layout Plain Layout |
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| 466 | |
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| 467 | field_A:interval_operation = "3600s" ; |
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| 468 | \end_layout |
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| 469 | |
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| 470 | \begin_layout Plain Layout |
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| 471 | |
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| 472 | field_A:interval_write = "6h" ; |
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| 473 | \end_layout |
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| 474 | |
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| 475 | \begin_layout Plain Layout |
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| 476 | |
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| 477 | field_A:coordinates = "time_centered axis_A nav_lat nav_lon" ; |
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| 478 | \end_layout |
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| 479 | |
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| 480 | \end_inset |
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| 481 | |
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| 482 | |
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| 483 | \end_layout |
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| 484 | |
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| 485 | \begin_layout Standard |
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| 486 | The data vary most quickly on dimension y, x which are two axes of domain_A. |
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| 487 | These are the default name of these dimension of a domain. |
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| 488 | The data on axis_C vary slower than on the domain and all the data are |
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| 489 | written one time step defined by time_counter at a time. |
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| 490 | \end_layout |
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| 491 | |
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| 492 | \begin_layout Standard |
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| 493 | Although a grid can be easily configured in XML file, it also needs defining |
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| 494 | in the FORTRAN via the definition of domain and axis for a model to work |
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| 495 | fully and correctly. |
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| 496 | All these instruction will be detailed in the next section. |
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| 497 | \end_layout |
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| 498 | |
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| 499 | \begin_layout Section |
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| 500 | Working with FORTRAN code |
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| 501 | \end_layout |
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| 502 | |
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| 503 | \begin_layout Standard |
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| 504 | Because grid is composed of domain and axis, all processing are taken grid |
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| 505 | via Domain and Axis. |
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| 506 | The next chapters supply the detail of these two sub components. |
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| 507 | |
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| 508 | \end_layout |
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| 509 | |
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| 510 | \end_body |
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| 511 | \end_document |
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