[yt-users] Athena phase plot problem

[John Zuhone]

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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-- 
John ZuHone

Postdoctoral Researcher
NASA/Goddard Space Flight Center

jzuhone at gmail.com
john.zuhone at nasa.gov
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