[yt-users] Analyzing DM-only data

Eric Hallman Eric.Hallman at colorado.edu
Tue Dec 22 12:07:33 PST 2009


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/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20091222/0ceae397/attachment.htm>


More information about the yt-users mailing list