[yt-users] Question about visualization of the derived Fields

Jun-Hwan Choi jhchoi at pa.uky.edu
Tue Apr 5 08:23:05 PDT 2011


Thank you Matthew for quick reply,

I made change from data.pf[Gamma] to data.pf["Gamma"], but it still 
crash with following report:
yt         INFO       2011-04-05 11:22:35,217 Loaded 501 total data outputs.
yt         INFO       2011-04-05 11:22:35,224 Parameters: 
current_time              = 0.0
yt         INFO       2011-04-05 11:22:35,224 Parameters: 
domain_dimensions         = [32, 32, 32]
yt         INFO       2011-04-05 11:22:35,224 Parameters: 
domain_left_edge          = [ 0.  0.  0.]
yt         INFO       2011-04-05 11:22:35,225 Parameters: 
domain_right_edge         = [ 1.  1.  1.]
yt         INFO       2011-04-05 11:22:35,225 Parameters: 
cosmological_simulation   = 0.0
yt         INFO       2011-04-05 11:22:35,225 Created plot collection 
with default plot-center = [0.5, 0.5, 0.5]
yt         INFO       2011-04-05 11:22:35,231 Getting the binary hierarchy
yt         INFO       2011-04-05 11:22:35,236 Finished with binary 
hierarchy reading
Warning: invalid value encountered in sqrt
Warning: invalid value encountered in sqrt
Traceback (most recent call last):
  File "plots.py", line 25, in <module>
    pc.add_slice("Temperature", 0)
  File 
"/home/jhchoi/common/src/yt-hg/yt/visualization/plot_collection.py", 
line 389, in add_slice
    center=center, **field_parameters)
  File 
"/home/jhchoi/common/src/yt-hg/yt/data_objects/data_containers.py", line 
732, in __init__
    self._refresh_data()
  File 
"/home/jhchoi/common/src/yt-hg/yt/data_objects/data_containers.py", line 
267, in _refresh_data
    self.get_data()
  File 
"/home/jhchoi/common/src/yt-hg/yt/data_objects/data_containers.py", line 
615, in get_data
    if self._generate_field(field):
  File 
"/home/jhchoi/common/src/yt-hg/yt/data_objects/data_containers.py", line 
638, in _generate_field
    self.pf.field_info[field].check_available(self)
  File 
"/home/jhchoi/common/src/yt-hg/yt/data_objects/field_info_container.py", 
line 276, in check_available
    validator(data)
  File 
"/home/jhchoi/common/src/yt-hg/yt/data_objects/field_info_container.py", 
line 374, in __call__
    raise NeedsDataField(doesnt_have)
yt.data_objects.field_info_container.NeedsDataField: (['Temperature'])

Thank you,
Junhwan

Matthew Turk wrote:
> Hi Junhwan,
>
> Your definition of the derived field looks okay to me, except that I
> think you need to do:
>
> data.pf["Gamma"]
>
> with the quotes around Gamma.  Additionally, it's usually quite
> helpful to have the crash report when diagnosing issues like these.
> :)
>
> -Matt
>
> On Tue, Apr 5, 2011 at 10:54 AM, Jun-Hwan Choi <jhchoi at pa.uky.edu> wrote:
>   
>> Thank you David and Matthew,
>>
>> I have looked the yt webpage about derived Field.
>> But, I can not find where in the script the definition goes.
>> For example I wrote the script to make slice as follow
>> ------------------------------------------------
>> from yt.mods import *
>> from yt.analysis_modules.api import EnzoSimulation
>> import matplotlib.pylab as pylab
>>
>> def _Temperature(field, data):
>>   DEFAULT_MU = 0.6
>>   return data["Gas_Energy"]*(data.pf[Gamma]-1)*DEFAULT_MU
>> add_field("Temperature", function=_Temperature)
>>
>> es = EnzoSimulation("RotatingSphere.enzo", initial_time=0.0, final_time=50.)
>>
>> time = []
>> i = 0
>> for output in es.allOutputs:
>>   # load up a dataset
>>   pf = load(output['filename'])
>>
>>
>>   # calculate the time of output
>>   time.append(0.1*i)
>>   i = i + 1
>>
>>   # create density slices
>>   pc = PlotCollection(pf, center=[0.5,0.5,0.5])
>>   pc.add_slice("Temperature", 0)
>>   pc.add_slice("Temperature", 2)
>>   pc.save("t%05.2f" % time[i-1])
>> --------------------------------------------------------------------
>> But this python script crashed.
>> How and where can I define new field in the script?
>>
>> Thank you
>> Junhwan
>>
>>
>> Matthew Turk wrote:
>>     
>>> Hi Junhwan,
>>>
>>> David wrote back earlier to your first email:
>>>
>>>
>>> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2011-April/001328.html
>>>
>>> Best,
>>>
>>> Matt
>>>
>>> On Mon, Apr 4, 2011 at 10:19 PM,  <jhchoi at pa.uky.edu> wrote:
>>>
>>>       
>>>> Hi YT uses,
>>>>
>>>> I would like to know how make slice, projection, or volume rendering
>>>> plots
>>>> for derived Fields.
>>>> For example, my enzo simulation output only has gas_energy (no
>>>> temperature
>>>> field in grid data) and I would like to make temperature map with
>>>> add_slice,
>>>> simply write add_slice("Temperature", 0) causes an error.
>>>> Is there any way this visualization can be done with derived Field?
>>>>
>>>> Thank you,
>>>> Junhwan
>>>>
>>>> --
>>>> --------------------------------------------------------------
>>>> Jun-Hwan Choi, Ph.D.
>>>> Department of Physics and Astronomy, University of Kentucky
>>>> Tel: (859) 897-6737        Fax: (859) 323-2846
>>>> Email: jhchoi at pa.uky.edu   URL: http://www.pa.uky.edu/~jhchoi
>>>> --------------------------------------------------------------
>>>>
>>>> ----------------------------------------------------------------
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>>>       
>> --
>> --------------------------------------------------------------
>> Jun-Hwan Choi, Ph.D.
>> Department of Physics and Astronomy, University of Kentucky
>> Tel: (859) 897-6737        Fax: (859) 323-2846
>> Email: jhchoi at pa.uky.edu   URL: http://www.pa.uky.edu/~jhchoi
>> --------------------------------------------------------------
>>
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-- 
--------------------------------------------------------------
Jun-Hwan Choi, Ph.D.
Department of Physics and Astronomy, University of Kentucky
Tel: (859) 897-6737        Fax: (859) 323-2846
Email: jhchoi at pa.uky.edu   URL: http://www.pa.uky.edu/~jhchoi
--------------------------------------------------------------




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