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

Matthew Turk matthewturk at gmail.com
Tue Apr 5 14:38:36 PDT 2011


Hi Junhwan,

I think I have figured out the issue, but I am not sure because I
don't have access to your data.

If you run this inside your loop:

print pf.h.field_list

You may see that you are missing the field "Gas_Energy", and you may
in its place have "TotalEnergy" or "Total_Energy" and possibly
"GasEnergy".  My guess is that what's happening is that the derived
field you defined can't be created, so rather than adding that to the
list of "known fields" it's falling back on the default definition for
Temperature, which is to read it from a file.

One option would be to switch on Gas_Energy in your problem definition
(from your parameter file I would guess you are using a homegrown
problem type) and you may even be able to have Enzo output the
temperature by examining how the OutputTemperatuer parameter works.

-Matt

On Tue, Apr 5, 2011 at 1:11 PM, Matthew Turk <matthewturk at gmail.com> wrote:
> Hi Junhwan,
>
> This is confusing to me.  Could you run:
>
> yt_lodgeit.py plots.py
>
> and then send me the location that it returns?  I'd like to
> investigate your script in detail, and I believe the best way to do
> that woul be to replicate it here.
>
> -Matt
>
> On Tue, Apr 5, 2011 at 11:23 AM, Jun-Hwan Choi <jhchoi at pa.uky.edu> wrote:
>> 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
>>>>>> --------------------------------------------------------------
>>>>>>
>>>>>> ----------------------------------------------------------------
>>>>>> This message was sent using IMP, the Internet Messaging Program.
>>>>>>
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>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
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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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>



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