[yt-users] Clump finder error

Caroline Van Borm borm at astro.rug.nl
Mon Jan 13 10:34:11 PST 2014


Hi Matt,

Thanks for your reply. There shouldn't be particles in my simulation, as 
far as I can tell.

Cheers,
Caroline



On 01/13/2014 06:21 PM, Matthew Turk wrote:
> Hi Caroline,
>
> Sorry you're having trouble!  Do you have particles in your simulation?
>
> -Matt
>
> On Fri, Jan 10, 2014 at 12:18 PM, Caroline Van Borm <borm at astro.rug.nl> wrote:
>> Hi all,
>>
>> I have a problem with the clump finder. When I try to run it on my dataset
>> (Enzo data), using a script that mostly follows the find_clumps.py from the
>> yt docs, I get the following, very long, error:
>>
>> Traceback (most recent call last):
>>    File "./findclumps.py", line 44, in <module>
>>      find_clumps(master_clump, c_min, c_max, step)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py",
>> line 182, in find_clumps
>>      find_clumps(clump, min_val*d_clump, max_val, d_clump)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py",
>> line 182, in find_clumps
>>      find_clumps(clump, min_val*d_clump, max_val, d_clump)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py",
>> line 182, in find_clumps
>>      find_clumps(clump, min_val*d_clump, max_val, d_clump)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py",
>> line 182, in find_clumps
>>      find_clumps(clump, min_val*d_clump, max_val, d_clump)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py",
>> line 182, in find_clumps
>>      find_clumps(clump, min_val*d_clump, max_val, d_clump)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py",
>> line 182, in find_clumps
>>      find_clumps(clump, min_val*d_clump, max_val, d_clump)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py",
>> line 182, in find_clumps
>>      find_clumps(clump, min_val*d_clump, max_val, d_clump)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py",
>> line 182, in find_clumps
>>      find_clumps(clump, min_val*d_clump, max_val, d_clump)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py",
>> line 182, in find_clumps
>>      find_clumps(clump, min_val*d_clump, max_val, d_clump)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py",
>> line 182, in find_clumps
>>      find_clumps(clump, min_val*d_clump, max_val, d_clump)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py",
>> line 182, in find_clumps
>>      find_clumps(clump, min_val*d_clump, max_val, d_clump)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py",
>> line 182, in find_clumps
>>      find_clumps(clump, min_val*d_clump, max_val, d_clump)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py",
>> line 182, in find_clumps
>>      find_clumps(clump, min_val*d_clump, max_val, d_clump)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py",
>> line 191, in find_clumps
>>      elif (child._isValid()):
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.py",
>> line 145, in _isValid
>>      self.function_value = eval(self.function)
>>    File "<string>", line 1, in <module>
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py",
>> line 94, in __call__
>>      return self._call_func_unlazy(args, kwargs)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py",
>> line 119, in _call_func_unlazy
>>      retval = self.func(self._data_source, *args, **kwargs)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py",
>> line 378, in _IsBound
>>      mass_to_use = data["TotalMass"]
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 332, in __getitem__
>>      self.get_data(key)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 2618, in get_data
>>      if self._generate_field(field):
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 362, in _generate_field
>>      self[field] = self.pf.field_info[field](self)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py",
>> line 395, in __call__
>>      dd = self._function(self, data)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/universal_fields.py",
>> line 444, in _TotalMass
>>      return (data["Density"]+data["particle_density"]) * data["CellVolume"]
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 332, in __getitem__
>>      self.get_data(key)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 2618, in get_data
>>      if self._generate_field(field):
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 359, in _generate_field
>>      self._generate_field_in_grids(field, ngt_exception.ghost_zones)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 369, in _generate_field_in_grids
>>      grid[field] = self.__touch_grid_field(grid, field)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 95, in save_state
>>      tr = func(self, grid, field, *args, **kwargs)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 373, in __touch_grid_field
>>      return grid[field]
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py",
>> line 157, in __getitem__
>>      self.get_data(key)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py",
>> line 200, in get_data
>>      self._generate_field(field)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py",
>> line 145, in _generate_field
>>      self[field] = self.pf.field_info[field](self)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py",
>> line 395, in __call__
>>      dd = self._function(self, data)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/universal_fields.py",
>> line 998, in _pdensity
>>      if data["particle_position_x"].size == 0: return blank
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py",
>> line 157, in __getitem__
>>      self.get_data(key)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py",
>> line 200, in get_data
>>      self._generate_field(field)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py",
>> line 145, in _generate_field
>>      self[field] = self.pf.field_info[field](self)
>>    File
>> "/home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py",
>> line 396, in __call__
>>      dd *= self._convert_function(data)
>> TypeError: unsupported operand type(s) for *=: 'NoneType' and 'float'
>>
>> The main difference is that for the function passed to Clump, I'm using
>> 'self.data.quantities["IsBound"](truncate=True,include_thermal_energy=True)
>>> 1.0' to find gravitationally bound objects.
>> When I run the clump finder on my data with a function that keeps clumps
>> based on the number of cells, it works fine.
>> I also tried running the script on the IsolatedGalaxy dataset as
>> demonstrated in the docs. This works fine too, also when the function is set
>> to the one mentioned above.
>>
>> Anyone knows what's going on here?
>> Btw, my yt version is b118390aa42c.
>>
>> Thanks!
>>
>> Cheers,
>> Caroline
>>
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