[yt-users] Analyzing DM-only data

Matthew Turk matthewturk at gmail.com
Tue Dec 22 15:37:42 PST 2009 

Hi Kai,

None of these can be plotted via slices -- slices only work on baryon
fields.  You can try pc.add_particles( ... ) -- you can get help on
this with help(pc.add_particles) .

The plotting capabilities of yt, I confess, are not terribly
well-suited to dark matter only simulations.  There are many analysis
tasks that will work with them, but yt is really better suited to
full, gas+dm simulations.  In the future I hope that the overall
DM-only plotting capabilities will be improved.  Stephen Skory may
have more information and suggestions about DM-only plots.

Additionally, we have a new version of the Cloud-in-Cell interpolation
method, written by Britton Smith, that is in the trunk and will be
released with yt-1.6 in the very near future.  This will allow
particles to be gridded and sliced through; however, as of right now,
it is only in the trunk.

-Matt

On Tue, Dec 22, 2009 at 5:27 PM,  <kcai at pa.uky.edu> wrote:
> Hi Matt and Eric,
>   Thank you for all this information; I have just tried with iyt:
> pf = load("RD0000/RD0000", data_style=6)
> pc = PlotCollection(pf, center=...)
> and then I ran
>
> print pf.h.field_list
>
> and got
> ['particle_velocity_z', 'particle_position_z', 'particle_position_x',
> 'particle_position_y', 'particle_index',
> 'particle_mass','particle_velocity_x', 'particle_velocity_y']
>
> so that worked.
> But then, when I tried with pc.add_slice('particle_position_y', 0)
> or 'particle_mass', I got seg faults...
> - which of the fields *can* I plot in x?
>
> Thanks,
> Kai
>
> Quoting Matthew Turk <matthewturk at gmail.com>:
>
>> Hi Kai,
>>
>> As a quick note (sorry for not kicking in earlier) if you are using
>> yt-1.5 you should be using data_style=6 , not
>> data_style='enzo_packed_3d'.  There was a change between 1.5 and the
>> current trunk, and the previous email message referred to the trunk.
>>
>> The import differences Eric noted above are new to me and I'm still
>> looking into them...
>>
>> Best,
>>
>> Matt
>>
>> On Tue, Dec 22, 2009 at 4:37 PM,  <kcai at pa.uky.edu> wrote:
>>>
>>> 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/
>>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ----------------------------------------------------------------
>>>>> This message was sent using IMP, the Internet Messaging Program.
>>>>
>>>> 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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