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<p class="MsoNormal"><span lang="EN-US">Dear all, <br>
<br>
I want to say thank you to all of you for making how powerful and convenient yt is. I really appreciate everything you have done.<br>
I’m now using yt 2.6 version and trying to construct our AMR code named “GAMER” frontend to yt. <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">So far I have several preliminary results that I could plot picture with projection /slice/ contour /radial profile successfully, and the outcome pictures all seem fine.
<br>
However when I tried to plot “3D Surface and Sketchfab”, I failed.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">It popped out some error messages. There exist some covering problems in my data structure. Actually this question also happened when I tried to plot “VorticityMagnitude”.
<br>
I couldn’t figure it out, and every data value and positions seem fine when I plot pictures in projection and slice.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Therefore, I believe there is some fundamental problem that I am too careless to pay attention to. Could anyone help me with this problem? Thank you in advance.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Jia-Hung Wu<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">The following is the error message.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">======================== Error Message ===========================================<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">“<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">In [75]: surface["Density"]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">yt : [ERROR ] 2014-06-06 22:49:12,262 Covering problem: 163 cells are uncovered<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">---------------------------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">KeyError Traceback (most recent call last)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><ipython-input-75-c8eab0fb4ee7> in <module>()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">----> 1 surface["Density"]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 316 if key not in self.fields:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 317 self.fields.append(key)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">--> 318 self.get_data(key)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 319 return self.field_data[key]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 320<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, sample_type)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 4233 my_verts = self._extract_isocontours_from_grid(<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 4234 g, self.surface_field, self.field_value,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">-> 4235 fields, sample_type)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 4236 if fields is not None:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 4237 my_verts, svals = my_verts<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 79 old_keys = grid.field_data.keys()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 80 grid.field_parameters = self.field_parameters<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">---> 81 tr = func(self, grid, field, *args, **kwargs)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 82 grid.field_parameters = old_params<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _extract_isocontours_from_grid(self, grid, field, value, sample_values, sample_type)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 4257 sample_type = "face"):<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 4258 mask = self.data_source._get_cut_mask(grid) * grid.child_mask<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">-> 4259 vals = grid.get_vertex_centered_data(field, no_ghost = False)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 4260 if sample_values is not None:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 4261 svals = grid.get_vertex_centered_data(sample_values)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in get_vertex_centered_data(self, field, smoothed, no_ghost)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 498 np.power(10.0, new_field, new_field)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 499 else:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">--> 500 cg = self.retrieve_ghost_zones(1, field, smoothed=smoothed)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 501 np.add(new_field, cg[field][1: ,1: ,1: ], new_field)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 502 np.add(new_field, cg[field][:-1,1: ,1: ], new_field)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in retrieve_ghost_zones(self, n_zones, fields, all_levels, smoothed)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 465 if smoothed:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 466 cube = self.hierarchy.smoothed_covering_grid(<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">--> 467 level, new_left_edge, **kwargs)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 468 else:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 469 cube = self.hierarchy.covering_grid(level, new_left_edge, **kwargs)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, *args, **kwargs)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3869 (self.pf.domain_right_edge - self.pf.domain_left_edge) /<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3870 self.pf.domain_dimensions.astype("float64"))<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">-> 3871 AMRCoveringGridBase.__init__(self, *args, **kwargs)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3872 self._final_start_index = self.global_startindex<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3873<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, level, left_edge, dims, fields, pf, num_ghost_zones, use_pbar, **kwargs)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3713 self.domain_width = np.rint((self.pf.domain_right_edge -<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3714 self.pf.domain_left_edge)/self.dds).astype('int64')<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">-> 3715 self._refresh_data()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3716<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3717 def _get_list_of_grids(self, buffer = 0.0):<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3730<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3731 def _refresh_data(self):<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">-> 3732 AMR3DData._refresh_data(self)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3733 self['dx'] = self.dds[0] * np.ones(self.ActiveDimensions, dtype='float64')<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3734 self['dy'] = self.dds[1] * np.ones(self.ActiveDimensions, dtype='float64')<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 304 """<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 305 self.clear_data()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">--> 306 self.get_data()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 307<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 308 def keys(self):<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, field)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3893 try:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3894 #print "Generating", field<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">-> 3895 self._generate_field(field)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3896 continue<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3897 except NeedsOriginalGrid, ngt_exception:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _generate_field(self, field)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3780 # First we check the validator; this might even raise!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3781 self.pf.field_info[field].check_available(self)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">-> 3782 self[field] = self.pf.field_info[field](self)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3783 else: # Can't find the field, try as it might<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3784 raise KeyError(field)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.pyc in __call__(self, data)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 383 ii = self.check_available(data)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 384 original_fields = data.keys() # Copy<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">--> 385 dd = self._function(self, data)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 386 dd *= self._convert_function(data)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 387 for field_name in data.keys():<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.pyc in _TranslationFunc(field, data)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 139 def TranslationFunc(field_name):<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 140 def _TranslationFunc(field, data):<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">--> 141 return data[field_name]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 142 return _TranslationFunc<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 143<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 316 if key not in self.fields:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 317 self.fields.append(key)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">--> 318 self.get_data(key)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 319 return self.field_data[key]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 320<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, field)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3935 n_bad = (self[field]==-999).sum()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3936 mylog.error("Covering problem: %s cells are uncovered", n_bad)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">-> 3937 raise KeyError(n_bad)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3938 if self._use_pbar: pbar.finish()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 3939<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">KeyError: 163<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">=========================================================================================<o:p></o:p></span></p>
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