[yt-users] TotalMass for ORION data
Nathan Goldbaum
nathan12343 at gmail.com
Mon May 6 16:55:43 PDT 2013
Hey Mark,
Clearly this behavior is undesirable and thanks for bringing it to our
attention. I'll file an issue so we can be sure to fix this before the
next major release.
For now, you should be able to get the desired effect with the following:
dd.quantities["TotalQuantity"]('CellMassMsun')
That will return the total gas mass in solar mass units. If you want it in
CGS or code units, just use 'CellMass' or 'CellMassCode' respectively
instead of 'CellMassMsun'. If you have any sink particles in your
simulation, they won't be included in the sum, so you'll have to do that by
hand.
-Nathan
On Mon, May 6, 2013 at 4:49 PM, Mark Krumholz <krumholz at ucolick.org> wrote:
>
> Hi All,
>
> I just updated to the latest version of yt, hoping that this would be
> fixed, but it seems not to be: the "TotalMass" function is broken for Orion
> data, and, from what I can tell, for any data set that doesn't contain dark
> matter particles. Here's what I get when I try to use it:
>
> In [1]: pf=load('data.0030.3d.hdf5')
> yt : [WARNING ] 2013-05-06 16:43:36,339 Setting 1.0 in code units to be
> 1.0 cm
> yt : [WARNING ] 2013-05-06 16:43:36,339 No time units. Setting 1.0 = 1
> second.
> yt : [INFO ] 2013-05-06 16:43:36,340 Parameters: current_time
> = 6.78585436617e+13
> yt : [INFO ] 2013-05-06 16:43:36,340 Parameters: domain_dimensions
> = [256 256 256]
> yt : [INFO ] 2013-05-06 16:43:36,341 Parameters: domain_left_edge
> = [ -1.68000000e+18 -1.68000000e+18 -1.68000000e+18]
> yt : [INFO ] 2013-05-06 16:43:36,341 Parameters: domain_right_edge
> = [ 1.68000000e+18 1.68000000e+18 1.68000000e+18]
>
> In [2]: dd=pf.h.all_data()
> ^[[Ayt : [INFO ] 2013-05-06 16:43:53,804 Adding unknown field
> gravitational-potential to list of fields
>
> In [3]: dd.quantities["TotalMass"]()
> ---------------------------------------------------------------------------
> KeyError Traceback (most recent call last)
> /home3/mkrumhol/yt-x86_64/src/yt-hg/scripts/iyt in <module>()
> ----> 1 dd.quantities["TotalMass"]()
>
> /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.pyc
> in __call__(self, *args, **kwargs)
> 90 self._data_source.pf.h.io)
> 91 if lazy_reader and not self.force_unlazy:
> ---> 92 return self._call_func_lazy(args, kwargs)
> 93 else:
> 94 return self._call_func_unlazy(args, kwargs)
>
> /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.pyc
> in _call_func_lazy(self, args, kwargs)
> 97 self.retvals = [ [] for i in range(self.n_ret)]
> 98 for gi,g in enumerate(self._get_grids()):
> ---> 99 rv = self.func(GridChildMaskWrapper(g,
> self._data_source), *args, **kwargs)
> 100 if not iterable(rv): rv = (rv,)
> 101 for i in range(self.n_ret):
> self.retvals[i].append(rv[i])
>
> /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.pyc
> in _TotalMass(data)
> 152 """
> 153 baryon_mass = data["CellMassMsun"].sum()
> --> 154 particle_mass = data["ParticleMassMsun"].sum()
> 155 return [baryon_mass + particle_mass]
> 156 def _combTotalMass(data, total_mass):
>
> /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.pyc
> in __getitem__(self, item)
> 58 def __getitem__(self, item):
> 59 if item not in self.local_cache:
> ---> 60 data = self.data_source._get_data_from_grid(self.grid,
> item)
> 61 self.local_cache[item] = data
> 62 return self.local_cache[item]
>
> /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in
> save_state(self, grid, field, *args, **kwargs)
> 93 old_keys = grid.field_data.keys()
> 94 grid.field_parameters = self.field_parameters
> ---> 95 tr = func(self, grid, field, *args, **kwargs)
> 96 grid.field_parameters = old_params
> 97 grid.field_data = YTFieldData( [(k, grid.field_data[k])
> for k in old_keys] )
>
> /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in
> _get_data_from_grid(self, grid, field)
> 2643 return np.array([f[i,:][pointI] for i in range(3)])
> 2644 else:
> -> 2645 tr = grid[field]
> 2646 if tr.size == 1: # dx, dy, dz, cellvolume
> 2647 tr = tr * np.ones(grid.ActiveDimensions,
> dtype='float64')
>
> /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in
> __getitem__(self, key)
> 155 """
> 156 if key not in self.field_data:
> --> 157 self.get_data(key)
> 158 return self.field_data[key]
> 159
>
> /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in
> get_data(self, field, convert)
> 198 else: raise
> 199 else:
> --> 200 self._generate_field(field)
> 201 return self.field_data[field]
> 202
>
> /home3/mkrumhol/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in
> _generate_field(self, field)
> 145 self[field] = self.pf.field_info[field](self)
> 146 else: # Can't find the field, try as it might
> --> 147 raise exceptions.KeyError(field)
> 148
> 149 def has_key(self, key):
>
> KeyError: 'ParticleMassMsun'
>
> This isn't a huge deal, because I can use "TotalQuantity" on "Density" as
> a workaround, but I thought I would report it.
>
> --
> Mark Krumholz
> krumholz at ucolick.org
>
>
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
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