[yt-dev] About Covering Problem while plotting 3D surface and sketchfab pictures

[吳佳鴻]

Dear all,

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.
I’m now using yt 2.6 version and trying to construct our AMR code named “GAMER” frontend to yt.
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.
However when I tried to plot “3D Surface and Sketchfab”, I failed.
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”.
I couldn’t figure it out, and every data value and positions seem fine when I plot pictures in projection and slice.
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.

Jia-Hung Wu


The following is the error message.
======================== Error Message ===========================================
“
In [75]: surface["Density"]
yt : [ERROR    ] 2014-06-06 22:49:12,262 Covering problem: 163 cells are uncovered
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-75-c8eab0fb4ee7> in <module>()
----> 1 surface["Density"]

/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key)
    316             if key not in self.fields:
    317                 self.fields.append(key)
--> 318             self.get_data(key)
    319         return self.field_data[key]
    320

/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)
   4233             my_verts = self._extract_isocontours_from_grid(
   4234                             g, self.surface_field, self.field_value,
-> 4235                             fields, sample_type)
   4236             if fields is not None:
   4237                 my_verts, svals = my_verts

/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)
     79         old_keys = grid.field_data.keys()
     80         grid.field_parameters = self.field_parameters
---> 81         tr = func(self, grid, field, *args, **kwargs)
     82         grid.field_parameters = old_params
     83         grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )

/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)
   4257                                        sample_type = "face"):
   4258         mask = self.data_source._get_cut_mask(grid) * grid.child_mask
-> 4259         vals = grid.get_vertex_centered_data(field, no_ghost = False)
   4260         if sample_values is not None:
   4261             svals = grid.get_vertex_centered_data(sample_values)

/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)
    498                 np.power(10.0, new_field, new_field)
    499         else:
--> 500             cg = self.retrieve_ghost_zones(1, field, smoothed=smoothed)
    501             np.add(new_field, cg[field][1: ,1: ,1: ], new_field)
    502             np.add(new_field, cg[field][:-1,1: ,1: ], new_field)

/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)
    465         if smoothed:
    466             cube = self.hierarchy.smoothed_covering_grid(
--> 467                 level, new_left_edge, **kwargs)
    468         else:
    469             cube = self.hierarchy.covering_grid(level, new_left_edge, **kwargs)

/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, *args, **kwargs)
   3869               (self.pf.domain_right_edge - self.pf.domain_left_edge) /
   3870                self.pf.domain_dimensions.astype("float64"))
-> 3871         AMRCoveringGridBase.__init__(self, *args, **kwargs)
   3872         self._final_start_index = self.global_startindex
   3873

/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)
   3713         self.domain_width = np.rint((self.pf.domain_right_edge -
   3714                     self.pf.domain_left_edge)/self.dds).astype('int64')
-> 3715         self._refresh_data()
   3716
   3717     def _get_list_of_grids(self, buffer = 0.0):

/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self)
   3730
   3731     def _refresh_data(self):
-> 3732         AMR3DData._refresh_data(self)
   3733         self['dx'] = self.dds[0] * np.ones(self.ActiveDimensions, dtype='float64')
   3734         self['dy'] = self.dds[1] * np.ones(self.ActiveDimensions, dtype='float64')

/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self)
    304         """
    305         self.clear_data()
--> 306         self.get_data()
    307
    308     def keys(self):

/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, field)
   3893                 try:
   3894                     #print "Generating", field
-> 3895                     self._generate_field(field)
   3896                     continue
   3897                 except NeedsOriginalGrid, ngt_exception:

/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _generate_field(self, field)
   3780             # First we check the validator; this might even raise!
   3781             self.pf.field_info[field].check_available(self)
-> 3782             self[field] = self.pf.field_info[field](self)
   3783         else: # Can't find the field, try as it might
   3784             raise KeyError(field)

/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.pyc in __call__(self, data)
    383         ii = self.check_available(data)
    384         original_fields = data.keys() # Copy
--> 385         dd = self._function(self, data)
    386         dd *= self._convert_function(data)
    387         for field_name in data.keys():

/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.pyc in _TranslationFunc(field, data)
    139 def TranslationFunc(field_name):
    140     def _TranslationFunc(field, data):
--> 141         return data[field_name]
    142     return _TranslationFunc
    143

/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key)
    316             if key not in self.fields:
    317                 self.fields.append(key)
--> 318             self.get_data(key)
    319         return self.field_data[key]
    320

/work1/ftd/yt_2.6_Version/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, field)
   3935                     n_bad = (self[field]==-999).sum()
   3936                     mylog.error("Covering problem: %s cells are uncovered", n_bad)
-> 3937                     raise KeyError(n_bad)
   3938         if self._use_pbar: pbar.finish()
   3939

KeyError: 163
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