[yt-users] Analyzing DM-only data
kcai at pa.uky.edu
kcai at pa.uky.edu
Tue Dec 22 13:37:44 PST 2009
Hi Eric,
Thanks for figuring it out. Then how do I load "lagos" under iyt?
Or I'll have to go with a script? You mentioned raven as well, but
then what is its relationship with lagos? I am a bit confused...
Thanks,
Kai
PS. sorry, but I only know very little YT (and nothing about python)...
Quoting Eric Hallman <Eric.Hallman at colorado.edu>:
> Ok, I am not 100% sure what is going on, I've only tried this a few
> times with dm_only, but I have noticed not too many other people are
> around, so I will tell you what I know.
>
> There are some quirky things with dm_only, for instance:
>
> if you start with
> from yt.mods import *
> pf = EnzoStaticOutput("datasetname",data_style="enzo_packed_3d")
>
> (or pf = load(...))
> the behavior of creating plot collections, reading field lists is
> different than if you use
>
> from yt.lagos import *
> pf = EnzoStaticOutput("datasetname",data_style="enzo_packed_3d")
>
> In the first case, if you type
>
> print pf.h.field_list
>
> it fails
>
> in the second case, it works. Unclear why.
>
> You can project quantities, or take slices, but not for all the
> particle quantities as they are (as near as I can tell). Some of the
> derived quantites (e.g. particle_density_pyx) can be projected without
> a problem, once you import raven. Though I am not the expert on the
> particle quantities, I seem to remember that you can only take slices/
> projections with grid quantities.
>
> Anyway, I would start with loading up the data by importing lagos
> first, loading the dataset, then check your field list and derived
> field list for what you want to make slices of. There is some more
> documentation on the enzotools site on how to manage particle data etc.
>
> Hopefully someone else can help with the real answers here at some point.
>
> Sorry I couldn't help more.
>
>
> On Dec 22, 2009, at 12:52 PM, kcai at pa.uky.edu wrote:
>
>> Hi Eric,
>>
>> Quoting Eric Hallman <Eric.Hallman at colorado.edu>:
>>
>>> Kai,
>>> I am getting a completely different error than you are, but I also
>>> fail at the same step. Which version of yt are you using?
>>>
>> I think it is yt-1.5, but I'm not 100% sure. I used the
>> installation script.
>>
>>> I will see if I can get this figured out.
>>>
>>>
>> Thank you for this!
>> Kai
>>
>>
>>> On Dec 22, 2009, at 11:58 AM, kcai at pa.uky.edu wrote:
>>>
>>>> Eric,
>>>> No, 'Dark_Matter_Density' does not work, either...
>>>> -> similar error:
>>>>
>>>> In [5]: pc.add_slice('Dark_Matter_Density', 0)
>>>> Exception AttributeError: "EnzoHierarchy instance has no
>>>> attribute '_data_file'" in <bound method EnzoHierarchy.__del__
>>>> of <yt.lagos.HierarchyType.EnzoHierarchy instance at
>>>> 0x2aa1cfbcf8>> ignored
>>>> ---------------------------------------------------------------------------
>>>> KeyError Traceback (most recent
>>>> call last)
>>>>
>>>> /share/home/kca223/src/yt-1.5/scripts/iyt in <module>()
>>>> ----> 1
>>>> 2
>>>> 3
>>>> 4
>>>> 5
>>>>
>>>> /share/home/kca223/src/yt-1.5/yt/raven/PlotCollection.pyc in
>>>> add_slice(self, *args, **kwargs)
>>>> 180 *fig_size* in (height_inches, width_inches)
>>>> 181 """
>>>> --> 182 return self.__add_slice(PlotTypes.SlicePlot,
>>>> *args, **kwargs)
>>>> 183
>>>> 184 def add_slice_interpolated(self, *args, **kwargs):
>>>>
>>>> /share/home/kca223/src/yt-1.5/yt/raven/PlotCollection.pyc in
>>>> __add_slice(self, ptype, field, axis, coord, center,
>>>> use_colorbar, figure, axes, fig_size, periodic, data_source,
>>>> **kwargs)
>>>> 204 coord = center[axis]
>>>> 205 if data_source is None:
>>>> --> 206 data_source = self.pf.hierarchy.slice(axis,
>>>> coord, field, center, **kwargs)
>>>> 207 p = self._add_plot(ptype(data_source, field,
>>>> use_colorbar=use_colorbar,
>>>> 208 axes=axes, figure=figure,
>>>>
>>>> /share/home/kca223/src/yt-1.5/yt/lagos/OutputTypes.pyc in
>>>> _get_hierarchy(self)
>>>> 144 if self._hierarchy_class == None:
>>>> 145 raise RuntimeError("You should not
>>>> instantiate StaticOutput.")
>>>> --> 146 self.__hierarchy =
>>>> self._hierarchy_class(self, data_style=self.data_style)
>>>> 147 return self.__hierarchy
>>>> 148
>>>>
>>>> /share/home/kca223/src/yt-1.5/yt/lagos/HierarchyType.pyc in
>>>> __init__(self, pf, data_style)
>>>> 689 break
>>>> 690 self.__guess_data_style(pf["TopGridRank"], testGrid,
>>>> testGridID)
>>>> --> 691 self._setup_data_queue()
>>>> 692 # For some reason, r8 seems to want Float64
>>>> 693 if pf.has_key("CompilerPrecision") \
>>>>
>>>> /share/home/kca223/src/yt-1.5/yt/lagos/HierarchyType.pyc in
>>>> _setup_data_queue(self)
>>>> 137
>>>> 138 def _setup_data_queue(self):
>>>> --> 139 self.queue = _data_style_funcs[self.data_style][5]()
>>>> 140
>>>> 141 def _setup_grid_corners(self):
>>>>
>>>> KeyError: 'enzo_packed_3d'
>>>>
>>>> I think it is I did not set the "data_style" right...
>>>>
>>>> Thanks,
>>>> Kai
>>>>
>>>>
>>>> Quoting Eric Hallman <Eric.Hallman at colorado.edu>:
>>>>
>>>>> ,
>>>>> I think the solution is that dark matter only runs do not have the
>>>>> field "Density", but only dark matter density is defined as a field.
>>>>> Density is a baryon field.
>>>>>
>>>>>
>>>>> On Dec 22, 2009, at 9:18 AM, kcai at pa.uky.edu wrote:
>>>>>
>>>>>> Sorry - forgot to change the subject of last email...
>>>>>>
>>>>>> Quoting kcai at pa.uky.edu:
>>>>>>
>>>>>>> Hi Matt,
>>>>>>> Last night I was browsing the archives of the yt-users list, and
>>>>>>> came across this thread of emails:
>>>>>>>
>>>>>>> [yt-users] corrupt enzo restart file?
>>>>>>> Matthew Turk matthewturk at gmail.com
>>>>>>> Thu Nov 12 09:30:36 PST 2009
>>>>>>>
>>>>>>> Hi Stephen,
>>>>>>>
>>>>>>> A problem with the way yt opens up dark matter only simulations is
>>>>>>> that the data_style has to be specified. This would be, for running
>>>>>>> on trunk, done with the parameter:
>>>>>>>
>>>>>>> data_style="enzo_packed_3d"
>>>>>>>
>>>>>>> to the StaticOutput initialization. Britton Smith has done some work
>>>>>>> recently on improving this, so he might be able to chime in with more
>>>>>>> info.
>>>>>>>
>>>>>>> -Matt
>>>>>>>
>>>>>>> On Thu, Nov 12, 2009 at 9:27 AM, Stephen Skory <stephenskory at
>>>>>>> yahoo.com> wrote:
>>>>>>>> Hi all,
>>>>>>>>
>>>>>>>> I am getting this error <http://paste.enzotools.org/show/257/
>>>>>>>> > when I attempt to instantiate the grid hierarchy.
>>>>>>> ......
>>>>>>>
>>>>>>>
>>>>>>> I am encountering the same "TypeError" when I tried to analyze
>>>>>>> a DM- only run.
>>>>>>> But I use iyt (the interactive yt) - how do I add the
>>>>>>> data_style then? I tried
>>>>>>> with
>>>>>>>
>>>>>>> pf = load("RD0000/RD0000", data_style="enzo_packed_3d")
>>>>>>> and then
>>>>>>> In [3]: pc = PlotCollection(pf, center=[0.5,0.5,0.5])
>>>>>>> yt INFO 2009-12-22 00:01:13,536 Created plot collection
>>>>>>> with default plot-center = [0.5, 0.5, 0.5]
>>>>>>>
>>>>>>> But when I tried to plot a slice, I got:
>>>>>>> In [4]: pc.add_slice("Density", 0)
>>>>>>> ---------------------------------------------------------------------------
>>>>>>> KeyError Traceback (most
>>>>>>> recent call last)
>>>>>>>
>>>>>>> /share/home/kca223/src/yt-1.5/scripts/iyt in <module>()
>>>>>>> ----> 1
>>>>>>> 2
>>>>>>> 3
>>>>>>> 4
>>>>>>> 5
>>>>>>>
>>>>>>> /share/home/kca223/src/yt-1.5/yt/raven/PlotCollection.pyc in
>>>>>>> add_slice(self, *args, **kwargs)
>>>>>>> 180 *fig_size* in (height_inches, width_inches)
>>>>>>> 181 """
>>>>>>> --> 182 return self.__add_slice(PlotTypes.SlicePlot,
>>>>>>> *args, **kwargs)
>>>>>>> 183
>>>>>>> 184 def add_slice_interpolated(self, *args, **kwargs):
>>>>>>>
>>>>>>> /share/home/kca223/src/yt-1.5/yt/raven/PlotCollection.pyc in
>>>>>>> __add_slice(self, ptype, field, axis, coord, center, use_colorbar,
>>>>>>> figure, axes, fig_size, periodic, data_source, **kwargs)
>>>>>>> 204 coord = center[axis]
>>>>>>> 205 if data_source is None:
>>>>>>> --> 206 data_source =
>>>>>>> self.pf.hierarchy.slice(axis, coord,
>>>>>>> field, center, **kwargs)
>>>>>>> 207 p = self._add_plot(ptype(data_source, field,
>>>>>>> use_colorbar=use_colorbar,
>>>>>>> 208 axes=axes, figure=figure,
>>>>>>>
>>>>>>> /share/home/kca223/src/yt-1.5/yt/lagos/OutputTypes.pyc in
>>>>>>> _get_hierarchy(self)
>>>>>>> 144 if self._hierarchy_class == None:
>>>>>>> 145 raise RuntimeError("You should not instantiate
>>>>>>> StaticOutput.")
>>>>>>> --> 146 self.__hierarchy = self._hierarchy_class(self,
>>>>>>> data_style=self.data_style)
>>>>>>> 147 return self.__hierarchy
>>>>>>> 148
>>>>>>>
>>>>>>> /share/home/kca223/src/yt-1.5/yt/lagos/HierarchyType.pyc in
>>>>>>> __init__(self, pf, data_style)
>>>>>>> 689 break
>>>>>>> 690 self.__guess_data_style(pf["TopGridRank"], testGrid,
>>>>>>> testGridID)
>>>>>>> --> 691 self._setup_data_queue()
>>>>>>> 692 # For some reason, r8 seems to want Float64
>>>>>>> 693 if pf.has_key("CompilerPrecision") \
>>>>>>>
>>>>>>> /share/home/kca223/src/yt-1.5/yt/lagos/HierarchyType.pyc in
>>>>>>> _setup_data_queue(self)
>>>>>>> 137
>>>>>>> 138 def _setup_data_queue(self):
>>>>>>> --> 139 self.queue = _data_style_funcs[self.data_style] [5] ()
>>>>>>> 140
>>>>>>> 141 def _setup_grid_corners(self):
>>>>>>>
>>>>>>> KeyError: 'enzo_packed_3d'
>>>>>>>
>>>>>>> Thanks a lot!
>>>>>>> Kai
>>>>>>>
>>>>>>
>>>>>>> This message was sent using IMP, the Internet Messaging Program.
>>>>>>
>>>>>>
>>>>>>
>>>>>> ----------------------------------------------------------------
>>>>>> This message was sent using IMP, the Internet Messaging Program.
>>>>>>
>>>>>> _______________________________________________
>>>>>> yt-users mailing list
>>>>>> yt-users at lists.spacepope.org
>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>
>>>>> Dr. Eric J. Hallman
>>>>> NSF Astronomy and Astrophysics Postdoctoral Fellow
>>>>> Center for Astrophysics and Space Astronomy
>>>>> University of Colorado at Boulder
>>>>> hallman (at) casa.colorado.edu
>>>>> Phone: (312) 725-4626
>>>>> http://solo.colorado.edu/~hallman/
>>>>
>>
>>
>>
>> ----------------------------------------------------------------
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>
> Dr. Eric J. Hallman
> NSF Astronomy and Astrophysics Postdoctoral Fellow
> Center for Astrophysics and Space Astronomy
> University of Colorado at Boulder
> hallman (at) casa.colorado.edu
> Phone: (312) 725-4626
> http://solo.colorado.edu/~hallman/
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