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- $ yt load cloud_hdf5_plt_cnt_0000
- yt : [WARNING ] 2013-07-05 13:05:05,266 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name
- yt : [INFO ] 2013-07-05 13:05:05,269 Parameters: current_time = 0.0
- yt : [INFO ] 2013-07-05 13:05:05,269 Parameters: domain_dimensions = [ 8 32 1]
- yt : [INFO ] 2013-07-05 13:05:05,270 Parameters: domain_left_edge = [ -2.46854420e+22 0.00000000e+00 -2.46854420e+22]
- yt : [INFO ] 2013-07-05 13:05:05,270 Parameters: domain_right_edge = [ 2.46854420e+22 1.97483536e+23 2.46854420e+22]
- yt : [INFO ] 2013-07-05 13:05:05,271 Parameters: cosmological_simulation = 0.0
- Python 2.7.4 (default, Jun 11 2013, 16:44:34)
- Type "copyright", "credits" or "license" for more information.
- IPython 0.13.1 -- An enhanced Interactive Python.
- ? -> Introduction and overview of IPython's features.
- %quickref -> Quick reference.
- help -> Python's own help system.
- object? -> Details about 'object', use 'object??' for extra details.
- In [1]: from yt.analysis_modules.level_sets.api import *
- In [2]: dd=pf.h.all_data()
- yt : [WARNING ] 2013-07-05 13:05:34,768 Dimensionality less than 3: reverting to overlap_proj
- In [3]: function='self.data["Density"].size>20'
- In [4]: master_clump = Clump(dd,None,"Density",function=function)
- yt : [INFO ] 2013-07-05 13:06:19,576 Getting field dens from 3648
- In [5]: find_clumps(master_clump,1.0e-29,1.0e-24,2.0)
- Finding clumps: min: 1.000000e-29, max: 1.000000e-24, step: 2.000000
- yt : [ERROR ] 2013-07-05 13:07:05,792 Covering problem: 181 cells are uncovered
- ---------------------------------------------------------------------------
- KeyError Traceback (most recent call last)
- /home/jforbes/yt-x86_64/src/yt-hg/yt/mods.py in <module>()
- ----> 1 find_clumps(master_clump,1.0e-29,1.0e-24,2.0)
- /home/jforbes/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py in find_clumps(clump, min_val, max_val, d_clump)
- 177 print "Finding clumps: min: %e, max: %e, step: %f" % (min_val, max_val, d_clump)
- 178 if min_val >= max_val: return
- --> 179 clump.find_children(min_val)
- 180
- 181 if (len(clump.children) == 1):
- /home/jforbes/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py in find_children(self, min_val, max_val)
- 118 if max_val is None: max_val = self.max_val
- 119 contour_info = identify_contours(self.data, self.field, min_val, max_val,
- --> 120 self.cached_fields)
- 121 for cid in contour_info:
- 122 new_clump = self.data.extract_region(contour_info[cid])
- /home/jforbes/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/contour_finder.py in identify_contours(data_source, field, min_val, max_val, cached_fields)
- 105 for gi,grid in enumerate(grids):
- 106 pbar.update(gi)
- --> 107 cg = grid.retrieve_ghost_zones(1, "tempContours", smoothed=False)
- 108 grid_set.update(set(cg._grids))
- 109 fd = cg["tempContours"].astype('int64')
- /home/jforbes/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py in retrieve_ghost_zones(self, n_zones, fields, all_levels, smoothed)
- 477 level, new_left_edge, **kwargs)
- 478 else:
- --> 479 cube = self.hierarchy.covering_grid(level, new_left_edge, **kwargs)
- 480
- 481 return cube
- /home/jforbes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py in __init__(self, level, left_edge, dims, fields, pf, num_ghost_zones, use_pbar, **kwargs)
- 3712 self.domain_width = np.rint((self.pf.domain_right_edge -
- 3713 self.pf.domain_left_edge)/self.dds).astype('int64')
- -> 3714 self._refresh_data()
- 3715
- 3716 def _get_list_of_grids(self, buffer = 0.0):
- /home/jforbes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py in _refresh_data(self)
- 3729
- 3730 def _refresh_data(self):
- -> 3731 AMR3DData._refresh_data(self)
- 3732 self['dx'] = self.dds[0] * np.ones(self.ActiveDimensions, dtype='float64')
- 3733 self['dy'] = self.dds[1] * np.ones(self.ActiveDimensions, dtype='float64')
- /home/jforbes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py in _refresh_data(self)
- 318 """
- 319 self.clear_data()
- --> 320 self.get_data()
- 321
- 322 def keys(self):
- /home/jforbes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py in get_data(self, fields)
- 3773 n_bad = np.where(self[obtain_fields[0]]==-999)[0].size
- 3774 mylog.error("Covering problem: %s cells are uncovered", n_bad)
- -> 3775 raise KeyError(n_bad)
- 3776
- 3777 def _generate_field(self, field):
- KeyError: 181
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