[yt-users] Athena phase plot problem

Stephanie Tonnesen stonnes at gmail.com
Tue Dec 18 10:21:28 PST 2012


Hi John,

So, what I mean by "expected" variables are basically all variables BUT
specific_scalar[0].  When I read in the vtk file, you can see that the
bottom line says

yt : [INFO     ] 2012-12-13 23:27:13,214 Adding unknown field
specific_scalar[0] to list of fields

Yes, I can do any of the "quantities" commands, for example:

alld = pf.h.all_data()
tracerp25 = alld.cut_region(["grid['specific_scalar[0]'] > 0.25",
"grid['z'] > 0.01"])

radmean = tracerp25.quantities["WeightedAverageQuantity"]("Radius","Ones")

Slicing also works:

p = SlicePlot(pf,"x","specific_scalar[0]")

Now I am starting to worry that it is because output is so big--each vtk
file is 72 MB, so a full output is almost 25 GB.  When I just use two
outputs (moving them so yt only sees id0 and id1 folders) the phase plot
works.  But, after running the add_phase_object command on the whole data
set for more than 1.5 hours I still have no result and my computer keeps
freezing--although top shows that only 42% of memory is being used.

Is it possible that my output is just too big?

Stephanie


On Tue, Dec 18, 2012 at 11:00 AM, John Zuhone <jzuhone at gmail.com> wrote:

> Hi Stephanie,
>
> Ok, thanks for checking that.
>
> I guess I'm not sure what you mean by the "expected" set of variables. Do
> you mean the ones that yt defines, or the ones that are in the field list?
> It looks like "velocity_z" works for one call and doesn't for another.
>
> Are you able to do anything else with "specific_scalar[0]"? Like make a
> slice, or a projection of some sort? Or maybe take the weighted average of
> it in a sphere. I'd be interested in seeing if the problem was restricted
> to phase plotting.
>
> How big is the dataset, by the way? Is there something that fails in the
> same way that the both of us can test on?
>
> Best,
>
> John
>
>
> On Tue, Dec 18, 2012 at 10:53 AM, Stephanie Tonnesen <stonnes at gmail.com>wrote:
>
>>
>> Hi,
>>
>> Yup.  Just to be sure I updated again and reattempted to make the
>> phase_object and python was Killed again.
>>
>> Thanks!
>>
>> Stephanie
>>
>>
>>
>> On Tue, Dec 18, 2012 at 12:35 AM, John ZuHone <jzuhone at gmail.com> wrote:
>>
>>> Hi Stephanie,
>>>
>>> Just want to make sure that you're using the latest version of the yt
>>> development tree--it contains some important Athena fixes that were put in
>>> a few weeks back.
>>>
>>> If so, then we'll work from there to figure out what's gone wrong.
>>>
>>> Best,
>>>
>>> John
>>>
>>> On Dec 17, 2012, at 5:44 PM, Stephanie Tonnesen <stonnes at gmail.com>
>>> wrote:
>>>
>>> Hi yt-users,
>>>
>>> I am trying to make phase_objects of Athena data.  I am able to make
>>> phase_objects if I use the "expected" set of variables (will show below),
>>> but kill my kernel or am kicked out of python if I try and use an "unknown
>>> field" read in from a set of vtk files.
>>>
>>>
>>>
>>> from yt.mods import *
>>>
>>> pf = load("id0/rps.0080.vtk")
>>>
>>> yt : [INFO     ] 2012-12-13 23:27:08,678 Temporarily setting domain_right_edge = -domain_left_edge. This will be corrected automatically if it is not the case.
>>> yt : [INFO     ] 2012-12-13 23:27:08,974 Parameters: current_time              = 40.00096
>>> yt : [INFO     ] 2012-12-13 23:27:08,974 Parameters: domain_dimensions         = [1048 1048  655]
>>> yt : [INFO     ] 2012-12-13 23:27:08,975 Parameters: domain_left_edge          = [-3.2 -3.2 -2. ]
>>> yt : [INFO     ] 2012-12-13 23:27:08,976 Parameters: domain_right_edge         = [ 3.2  3.2  2. ]
>>> yt : [INFO     ] 2012-12-13 23:27:08,977 Parameters: cosmological_simulation   = 0.0
>>> yt : [INFO     ] 2012-12-13 23:27:13,214 Adding unknown field specific_scalar[0] to list of fields
>>>
>>> pf.h.field_list
>>>
>>> ['density',
>>>  'pressure',
>>>  'velocity_z',
>>>  'velocity_x',
>>>  'velocity_y',
>>>  'specific_scalar[0]']
>>>
>>> alld = pf.h.all_data()
>>> tracerp25 = alld.cut_region(["grid['specific_scalar[0]'] > 0.25",
>>> "grid['z'] > 0.01"])
>>>
>>> ##These commands works:
>>>
>>> radmean = tracerp25.quantities["WeightedAverageQuantity"]("Radius","Ones")
>>>
>>> pc = PlotCollectionInteractive(pf)
>>>
>>> pc.add_phase_object(alld,["z","velocity_z","CellMass"],weight=None)
>>>
>>> #The calls below fail.  There is no error message.  If I am in iPython,
>>> #the kernel dies.  If I am running on a computer, it freezes and
>>> #eventually I just get the message
>>> #Killed
>>>
>>> pc.add_phase_object(alld,["z","specific_scalar[0]","CellMass"],weight=None)
>>> pc.add_phase_object(tracerp25,["z","velocity_z","CellMass"],weight=None)
>>>
>>> #If I read in a single vtk file ("id122/rps-id122.0080.vtk") the above
>>> #commands work
>>>
>>> Any help would be much appreciated!  Thanks,
>>>
>>> Stephanie
>>> _______________________________________________
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>>>
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>>
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>
>
> --
> John ZuHone
>
> Postdoctoral Researcher
> NASA/Goddard Space Flight Center
>
> jzuhone at gmail.com
> john.zuhone at nasa.gov
>
>
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