source: branches/ORCHIDEE_2_2/ORCHIDEE/src_xml/context_input_orchidee.xml @ 8367

Last change on this file since 8367 was 8133, checked in by josefine.ghattas, 11 months ago
  • Updated to use module hdf5/1.12.2 needed at irene-skl, previously done in coupled configuration. Needed for XIOS3.
  • Cleaning in xml files needed for use with XIOS3. All modifications are also working with XIOS2.

See ticket #933
  • Property svn:keywords set to Date Revision HeadURL
File size: 21.7 KB
Line 
1<!-- =========================================================================================================== -->
2<!-- ORCHIDEE context for input files                                                                            -->
3<!-- context_input_orchidee.xml : Configuration file for ORCHIDEE for reading of input files using XIOS          -->
4<!-- This file must be included from iodef.xml                                                                   -->
5<!-- All specifications specific for the reading and interpolating of input files are regrouped in this file.    -->
6<!-- Find below sections for file_definition, field_definition, domain_definition, grid_definition and           -->
7<!-- variable_definition.                                                                                        -->   
8<!-- Recent change:  added block to read params_sp_mip.nc (Salma Tafasca and Agnes Ducharne, November 2020)      -->
9<!--                                                                                                             --> 
10<!-- $HeadURL$          -->
11<!-- $Date$                                                      -->
12<!-- $Revision$                                                                                           -->
13<!-- =========================================================================================================== -->
14<context id="orchidee">
15
16
17  <!-- ========================================================================================================= -->
18  <!-- Definition of input files                                                                                 -->
19  <!-- The input files are activated or desactivated from the source code depending on simulation set up.        -->
20  <!-- The variables are here on the input source grid.                                                          -->
21  <!-- Different treatment are done accordig to the file.                                                        -->
22  <!-- Values higher than 1e10 are for some files considered as missing values and the field is then set to 0.   -->
23  <!-- A normalization are sometimes done with the fraction of the grid cell.                                    -->
24  <!-- Sometimes, if only missing values are found for a grid cell, then a default value is set.                 -->
25  <!-- ========================================================================================================= -->
26 
27  <file_definition>
28
29    <file id="soils_param_file" mode="read" output_freq="1y" enabled="true">
30      <field id="soilcolor" name="soilcolor" domain_ref="dom_file_soil" operation="instant" freq_offset="1ts" enabled="false"/>
31      <field id="soiltext" name="soiltext" domain_ref="dom_file_soil" operation="instant" freq_offset="1ts"/>
32    </file>
33
34    <!-- Default file name: params_sp_mip.nc for both all soil hydraulic parameters. -->
35    <!--file id="soilparam_file" mode="read" output_freq="1y" enabled="true"-->
36      <!--field id="soilks" name="soilks" domain_ref="dom_file_soil" operation="instant" freq_offset="1ts" > this &gt; $min_sechiba ? 1e10 : 0 </field-->
37      <!--field id="soilnvan" name="soilnvan" domain_ref="dom_file_soil" operation="instant" freq_offset="1ts" > this &gt; $min_sechiba ? 1e10 : 0 </field-->
38      <!--field id="soilavan" name="soilavan" domain_ref="dom_file_soil" operation="instant" freq_offset="1ts" > this &gt; $min_sechiba ? 1e10 : 0 </field-->
39      <!--field id="soilmcr" name="soilmcr" domain_ref="dom_file_soil" operation="instant" freq_offset="1ts" > this &gt; $min_sechiba ? 1e10 : 0 </field-->
40      <!--field id="soilmcs" name="soilmcs" domain_ref="dom_file_soil" operation="instant" freq_offset="1ts" > this &gt; $min_sechiba ? 1e10 : 0 </field-->
41      <!--field id="soilmcfc" name="soilmcfc" domain_ref="dom_file_soil" operation="instant" freq_offset="1ts" > this &gt; $min_sechiba ? 1e10 : 0 </field-->
42      <!--field id="soilmcw" name="soilmcw" domain_ref="dom_file_soil" operation="instant" freq_offset="1ts" > this &gt; $min_sechiba ? 1e10 : 0 </field-->
43    <!--/file-->
44   
45    <file  id="PFTmap_file"  mode="read" output_freq="1y">
46      <field id="maxvegetfrac_read"  name="maxvegetfrac" domain_ref="dom_file_pft" axis_ref="nvm" operation="instant"  freq_offset="1ts"> this &lt; 1e10 ? this : 0 </field>
47      <field id="maxvegetfrac_mask"  name="maxvegetfrac" domain_ref="dom_file_pft" axis_ref="nvm" operation="instant"  freq_offset="1ts"> this &lt; 1e10 ? 1 : 0 </field>
48    </file>
49   
50    <file id="topography_file"  mode="read" output_freq="1y">
51      <!--      <field id="pente"  domain_ref="dom_file_topo"  operation="instant"  freq_offset="1ts" > (this &gt; 1e10) ? 1 : this </field>     ==> In reference, missing value are use for computing, this probably wrong -->
52      <field id="pente_read"       name="pente" domain_ref="dom_file_topo"  operation="instant"  freq_offset="1ts" > ((this/$slope_noreinf) &lt; 1)? this/$slope_noreinf : 1 </field>
53      <field id="mask_pente_read"  name="pente" domain_ref="dom_file_topo"  operation="instant"  freq_offset="1ts" > (this &lt; $min_sechiba)? 0 : 1                         </field>  <!-- create mask -->
54    </file>
55   
56    <file id="albedo_file" mode="read" output_freq="1y">
57      <field id="mask_alb_read"    name="mask"       domain_ref="dom_file_albedo"  operation="instant"  freq_offset="1ts" />
58      <field id="bg_alb_vis_read"  name="bg_alb_vis" domain_ref="dom_file_albedo"  operation="instant"  freq_offset="1ts" >  mask_alb_read &gt; 0.99 ? this : $missing_value  </field>
59      <field id="bg_alb_nir_read"  name="bg_alb_nir" domain_ref="dom_file_albedo"  operation="instant"  freq_offset="1ts" >  mask_alb_read &gt; 0.99 ? this : $missing_value  </field>
60    </file>
61   
62    <file id="lai_file" mode="read" output_freq="1y" time_counter_name="toto" cyclic="true">
63      <field id="lai_read"       name="LAI" grid_ref="lai" operation="instant"  freq_offset="1ts" > this &gt; 20 ? 0 : this </field>
64      <field id="mask_lai_read"  name="LAI" grid_ref="lai" operation="instant"  freq_offset="1ts" > this &gt; 20 ? 0 : 1    </field>  <!-- create mask -->
65    </file>
66
67    <file id="fertilizer_file" mode="read" output_freq="1y" cyclic="true">
68      <field id="N_qt_OTHER_year_read"  name="N_qt_OTHER_year" domain_ref="dom_file_fertilizer" operation="instant"  freq_offset="1ts"/>
69      <field id="N_qt_WRICE_year_read"  name="N_qt_WRICE_year" domain_ref="dom_file_fertilizer" operation="instant"  freq_offset="1ts"/>
70    </file>
71   
72    <file id="bbg_clim_file" mode="read" output_freq="1y" cyclic="true">
73      <field id="flx_co2_bbg_year_read"  name="flx_co2_bbg_year" domain_ref="dom_file_bbg_clim" operation="instant"  freq_offset="1ts"/>
74    </file>
75   
76    <file id="reftemp_file" mode="read" output_freq="1y" cyclic="true">
77      <field id="reftemp_read"  name="temperature" domain_ref="dom_file_reftemp" operation="instant"  freq_offset="1ts"/>
78    </file>
79   
80    <file id="woodharvest_file" mode="read" output_freq="1y" cyclic="true">
81      <field id="woodharvest_read"  name="woodharvest" domain_ref="dom_file_woodharvest" operation="instant"  freq_offset="1ts"/>
82    </file>
83   
84       
85    <file id="nudge_moistc" name="nudge_moistc" type="one_file" mode="read" output_freq="1d">
86      <field  id="moistc_in" name="moistc" operation="instant" grid_ref="grid_file_moistc" freq_offset="1ts" > (this &gt; 1e10) ? 0 : this </field>
87      <field  id="mask_moistc_in" name="moistc" operation="instant" grid_ref="grid_file_moistc" freq_offset="1ts" > (this &gt; 1e10) ? 0 : 1 </field>
88    </file>
89   
90    <file id="nudge_snow" name="nudge_snow" type="one_file" mode="read" output_freq="1d">
91      <field  id="snowdz_in" name="snowdz" operation="instant" grid_ref="grid_file_snow" freq_offset="1ts" > (this &gt; 1e10) ? 0 : this </field>
92      <field  id="snowrho_in" name="snowrho" operation="instant" grid_ref="grid_file_snow" freq_offset="1ts" > (this &gt; 1e10) ? 0 : this </field>
93      <field  id="snowtemp_in" name="snowtemp" operation="instant" grid_ref="grid_file_snow" freq_offset="1ts" > (this &gt; 1e10) ? 0 : this </field>
94      <field  id="mask_snow_in" name="snowdz" operation="instant" grid_ref="grid_file_snow" freq_offset="1ts" > (this &gt; 1e10) ? 0 : 1 </field>
95    </file>
96   
97  </file_definition>
98
99
100  <!-- ========================================================================================================= -->
101  <!-- Definition of all field coming from files but now interpolated to the model grid.                         -->
102  <!-- ========================================================================================================= -->
103
104  <field_definition>
105
106    <field_group enabled="false" read_access="true">
107
108      <field_group id="soil_color" enabled="false">
109        <field id="soilcolor0" field_ref="soilcolor" domain_ref="dom_from_soil" > soilcolor == 0 </field>
110        <field id="soilcolor1" field_ref="soilcolor" domain_ref="dom_from_soil" > soilcolor == 1 </field>
111        <field id="soilcolor2" field_ref="soilcolor" domain_ref="dom_from_soil" > soilcolor == 2 </field>
112        <field id="soilcolor3" field_ref="soilcolor" domain_ref="dom_from_soil" > soilcolor == 3 </field>
113        <field id="soilcolor4" field_ref="soilcolor" domain_ref="dom_from_soil" > soilcolor == 4 </field>
114        <field id="soilcolor5" field_ref="soilcolor" domain_ref="dom_from_soil" > soilcolor == 5 </field>
115        <field id="soilcolor6" field_ref="soilcolor" domain_ref="dom_from_soil" > soilcolor == 6 </field>
116        <field id="soilcolor7" field_ref="soilcolor" domain_ref="dom_from_soil" > soilcolor == 7 </field>
117        <field id="soilcolor8" field_ref="soilcolor" domain_ref="dom_from_soil" > soilcolor == 8 </field>
118        <field id="soilcolor9" field_ref="soilcolor" domain_ref="dom_from_soil" > soilcolor == 9 </field>
119      </field_group>
120
121      <field_group id="soil_text" field_ref="soiltext" domain_ref="dom_from_soil" enabled="true" read_access="true">
122        <field id="soiltext1"  > soiltext == 1 </field>
123        <field id="soiltext2"  > soiltext == 2 </field>
124        <field id="soiltext3"  > soiltext == 3 </field>
125        <field id="soiltext4"  > soiltext == 4 </field>
126        <field id="soiltext5"  > soiltext == 5 </field>
127        <field id="soiltext6"  > soiltext == 6 </field>
128        <field id="soiltext7"  > soiltext == 7 </field>
129        <field id="soiltext8"  > soiltext == 8 </field>
130        <field id="soiltext9"  > soiltext == 9 </field>
131        <field id="soiltext10" > soiltext == 10 </field>
132        <field id="soiltext11" > soiltext == 11 </field>
133        <field id="soiltext12" > soiltext == 12 </field>
134        <field id="soiltext13" > soiltext == 13 </field>
135      </field_group>
136     
137      <field id="frac_veget"      field_ref="maxvegetfrac_read" domain_ref="dom_from_pft" read_access="true" enabled="true" />
138      <field id="frac_veget_frac" field_ref="maxvegetfrac_mask" domain_ref="dom_from_pft" read_access="true" enabled="true" />
139
140      <field id="slope_tmp"           field_ref="pente_read"       domain_ref="dom_from_topo_read"                                  />
141      <field id="frac_slope_interp"   field_ref="mask_pente_read"  domain_ref="dom_from_topo_read" read_access="true" enabled="true"/>
142      <field id="reinf_slope_interp"                               domain_ref="dom_from_topo" read_access="true" enabled="true"> (frac_slope_interp &gt; $min_sechiba ) ? 1-slope_tmp/(frac_slope_interp+1e-100) : $slope_default </field>
143
144      <field id="bg_alb_vis_tmp"   field_ref="bg_alb_vis_read"  domain_ref="dom_from_albedo"  />
145      <field id="bg_alb_vis_interp" field_ref="bg_alb_vis_tmp"  read_access="true" enabled="true" > this == $missing_value ? $albbg_vis_default : this </field>
146
147      <field id="bg_alb_nir_tmp"    field_ref="bg_alb_nir_read"  domain_ref="dom_from_albedo"  />
148      <field id="bg_alb_nir_interp" field_ref="bg_alb_nir_tmp"  read_access="true"  enabled="true" >  this == $missing_value ? $albbg_nir_default : this </field>
149     
150      <field id="lai_tmp"          field_ref="lai_read"      grid_ref="grid_from_lai" />
151      <field id="frac_lai_interp"  field_ref="mask_lai_read" grid_ref="grid_from_lai" read_access="true" enabled="true" />
152      <field id="lai_interp"       field_ref="lai_tmp"                           read_access="true" enabled="true"  >  lai_tmp/(frac_lai_interp+1e-100) </field>  <!-- renormalize -->
153     
154      <field id="N_qt_WRICE_year_interp"  field_ref="N_qt_WRICE_year_read"  domain_ref="dom_from_fertilizer" read_access="true" enabled="true" />
155      <field id="N_qt_OTHER_year_interp"  field_ref="N_qt_OTHER_year_read"  domain_ref="dom_from_fertilizer" read_access="true" enabled="true" />
156     
157      <field id="flx_co2_bbg_year_interp"  field_ref="flx_co2_bbg_year_read"  domain_ref="dom_from_bbg_clim" read_access="true" enabled="true" />
158
159      <field id="reftemp_interp"  field_ref="reftemp_read"  domain_ref="dom_from_reftemp" read_access="true" enabled="true" />
160
161      <field id="woodharvest_interp"  field_ref="woodharvest_read"  domain_ref="dom_from_woodharvest" read_access="true" enabled="true" />
162     
163    </field_group>
164
165    <field_group id="orchidee_input_mc" grid_ref="grid_nslm_nstm_read">
166      <!-- Interpolate the mask. This gives now the fraction of the source area underlaying the model grid cell -->
167      <field id="mask_moistc_interp" field_ref="mask_moistc_in" read_access="true" />
168      <!-- Interpolate the variable. Note that where the source file had missing values, the variables was set to 0. Therefor normalization is needed.     -->
169      <!-- Normalize the interpolated values with the mask which corresponds to the fraction of underlaying valid source grid cells.                       -->
170      <!-- The default value 0.2 is used if the mask is 0. This is the case if no information at all was found on the source grid for the model grid cell. -->
171      <field id="moistc_tmp" field_ref="moistc_in"  />
172      <field id="moistc_interp" field_ref="moistc_tmp" read_access="true" > (mask_moistc_interp &lt; 1e-4) ? 0.2 : this/(mask_moistc_interp+1e-100) </field>
173    </field_group>
174
175    <field_group id="orchidee_input_snow" grid_ref="grid_nsnow2" >
176      <field id="mask_snow_interp" field_ref="mask_snow_in" read_access="true" />
177      <field id="snowdz_tmp" field_ref="snowdz_in" />
178      <!-- Set snowdz=0 where no information found on source grid, for all other points normlize with the fracion of underlaying source grid cells      -->
179      <field id="snowdz_interp" field_ref="snowdz_tmp" read_access="true" > (mask_snow_interp &lt; 1e-4) ? 0 : this/(mask_snow_interp+1e-100) </field>
180      <field id="snowrho_tmp" field_ref="snowrho_in" />
181      <!-- Set snowrho=50 where no information found on source grid, for all other points normlize with the fracion of underlaying source grid cells    -->
182      <field id="snowrho_interp" field_ref="snowrho_tmp" read_access="true" > (mask_snow_interp &lt; 1e-4) ? 50 : this/(mask_snow_interp+1e-100) </field>
183      <field id="snowtemp_tmp" field_ref="snowtemp_in" />
184      <!-- Set snowtemp=273 where no information found on source grid, for all other points normlize with the fracion of underlaying source grid cells  -->
185      <field id="snowtemp_interp" field_ref="snowtemp_tmp" read_access="true" > (mask_snow_interp &lt; 1e-4) ? 273 : this/(mask_snow_interp+1e-100) </field>
186    </field_group>
187 
188  </field_definition>
189
190
191
192  <!-- =========================================================================================================== -->
193  <!-- Definition of a horizontal domain for each input file                                                       -->
194  <!-- 2 different domains are specified for each input file X: dom_file_X and dom_from_X                          -->
195  <!--                                                                                                             -->
196  <!-- dom_file_X is the horizontal original grid in the input file. In this domain, specifications to help XIOS   -->
197  <!-- read the grid can be added such as generate_rectilinear_domain                                              -->
198  <!--                                                                                                             -->
199  <!-- dom_from_X describes how to make the interpolation from the file to the model grid. This domain contains    -->
200  <!-- the interpolation methode specific to the file.                                                             -->
201  <!--                                                                                                             -->
202  <!-- If the variable contains more dimensions than the horizontal domain and 1 axis, 2 grids must be specified:  -->
203  <!-- One for the orignial grid in the input file and one for the interpolation to model grid. These two grids    -->
204  <!-- uses 2 domains specified as above.                                                                          -->
205  <!-- We here suppose that the interpolation is only done on the horizontal domain                                -->
206  <!-- =========================================================================================================== -->
207
208  <domain_definition>
209
210    <domain id="dom_file_moistc" type="rectilinear">
211      <generate_rectilinear_domain />
212    </domain>
213   
214    <domain id="dom_file_snow" type="rectilinear">
215      <generate_rectilinear_domain />
216    </domain>
217   
218    <domain id="dom_from_soil" domain_ref="domain_landpoints">
219      <interpolate_domain order="1" renormalize="false"/>
220    </domain>
221
222    <domain id="dom_from_pft" domain_ref="domain_landpoints">
223      <interpolate_domain order="1" renormalize="false" />
224    </domain>
225   
226    <domain id="dom_from_topo" domain_ref="domain_landpoints">
227    </domain>
228   
229    <domain id="dom_from_topo_read" domain_ref="domain_landpoints">
230      <interpolate_domain order="1" renormalize="false" />
231    </domain>
232
233    <domain id="dom_from_albedo" domain_ref="domain_landpoints">
234      <interpolate_domain order="1" renormalize="true" detect_missing_value="true"/>
235    </domain>
236   
237    <domain id="dom_from_lai" domain_ref="domain_landpoints">
238      <interpolate_domain order="1" renormalize="false" />
239    </domain>
240   
241    <domain id="dom_from_bbg_clim" domain_ref="domain_landpoints">
242      <interpolate_domain order="1" renormalize="false" />
243    </domain>
244   
245    <domain id="dom_from_fertilizer" domain_ref="domain_landpoints">
246      <interpolate_domain order="1" renormalize="false" />
247    </domain>
248   
249    <domain id="dom_from_reftemp" domain_ref="domain_landpoints">
250      <interpolate_domain order="1" renormalize="false" />
251    </domain>
252   
253    <domain id="dom_from_woodharvest" domain_ref="domain_landpoints">
254      <interpolate_domain order="1" renormalize="false" />
255    </domain>
256   
257    <domain id="dom_file_soil" type="rectilinear">
258      <!-- generate_rectilinear_domain bounds_lon_start="-180" bounds_lon_end="180" bounds_lat_start="-90" bounds_lat_end="90"/-->
259      <generate_rectilinear_domain bounds_lon_start="-180" bounds_lon_end="180" bounds_lat_start="90" bounds_lat_end="-90"/>
260    </domain>
261   
262    <domain id="dom_file_pft" type="rectilinear">
263      <generate_rectilinear_domain/>
264    </domain>
265   
266    <domain id="dom_file_topo" type="rectilinear">
267      <generate_rectilinear_domain/>
268    </domain>
269   
270    <domain id="dom_file_albedo" type="rectilinear">
271      <generate_rectilinear_domain />
272    </domain>
273   
274    <domain id="dom_file_lai" type="rectilinear">
275      <generate_rectilinear_domain/>
276    </domain>
277   
278    <domain id="dom_file_bbg_clim" type="rectilinear">
279      <generate_rectilinear_domain/>
280    </domain>
281   
282    <domain id="dom_file_fertilizer" type="rectilinear">
283      <generate_rectilinear_domain/>
284    </domain>
285
286    <domain id="dom_file_reftemp" type="rectilinear">
287      <generate_rectilinear_domain bounds_lon_start="-180" bounds_lon_end="180" bounds_lat_start="90" bounds_lat_end="-90"/>
288    </domain>
289
290    <domain id="dom_file_woodharvest" type="rectilinear">
291      <generate_rectilinear_domain/>
292    </domain>
293   
294  </domain_definition>
295
296
297  <!-- =========================================================================================================== -->
298  <!-- Definition of input grids and interpolated grids                                                            -->
299  <!-- =========================================================================================================== -->
300
301  <grid_definition>
302
303    <grid id="grid_file_moistc">
304      <domain domain_ref="dom_file_moistc"/>
305      <axis axis_ref="nslm" />
306      <axis axis_ref="nstm" />
307    </grid> 
308
309    <grid id="grid_file_snow">
310      <domain domain_ref="dom_file_snow"/>
311      <axis axis_ref="nsnow" />
312    </grid> 
313   
314    <grid id="grid_from_lai">
315      <domain domain_ref="dom_from_lai" />
316      <axis axis_ref="nvm" />
317      <axis axis_ref="lai_time" />
318    </grid>
319   
320    <grid id="lai">
321      <domain domain_ref="dom_file_lai" />
322      <axis axis_ref="nvm" />
323      <axis axis_ref="lai_time" />
324    </grid>
325   
326    <grid id="grid_nsnow2">
327      <domain domain_ref="domain_landpoints" >
328        <interpolate_domain order="1"/>
329      </domain>
330      <axis axis_ref="nsnow" />
331    </grid>
332
333  </grid_definition>
334 
335 
336  <!-- =========================================================================================================== -->
337  <!-- Variable denfinition needed for interpolation of input files                                                -->
338  <!-- The values for below variables are set from the fortran code.                                               -->
339  <!-- =========================================================================================================== -->
340
341  <variable_definition>
342   
343    <variable id="slope_default" type="double">xxx</variable>
344    <variable id="slope_noreinf" type="double">xxx</variable>
345    <variable id="min_sechiba" type="double">xxx</variable>
346    <variable id="albbg_vis_default" type="double">xxx</variable>
347    <variable id="albbg_nir_default" type="double">xxx</variable>
348   
349  </variable_definition>
350 
351
352</context>
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