[yt-users] Analyzing DM-only data

Matthew Turk matthewturk at gmail.com
Tue Dec 22 13:40:14 PST 2009 

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/
>
>
>
> ----------------------------------------------------------------
> 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
>

More information about the yt-users mailing list