[yt-users] particle angular momentum profile error and accumulation profile
Junhwan Choi (최준환)
choi.junhwan at gmail.com
Wed Jan 27 11:53:00 PST 2016
Do I just update my yt to get this fix?
Junhwan
On Wed, Jan 27, 2016 at 1:49 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
> I've fixed it for you. Thanks for filing the issue!
>
> On Wed, Jan 27, 2016 at 1:39 PM, Junhwan Choi (최준환)
> <choi.junhwan at gmail.com> wrote:
>> Hi Nathan,
>>
>> I just created issue.
>> Accidentally, I made two same issues (w/ and w/o attached file), 1163 and 1164.
>> Is there anyway that I can tell the issue is the resolved and I can
>> update my version?
>>
>> Thank you,
>> Junhwan
>>
>>
>>
>> On Wed, Jan 27, 2016 at 1:23 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>>> This seems like a bug. Any chance you can file an issue about it:
>>>
>>> https://bitbucket.org/yt_analysis/yt/issues/new
>>>
>>> Please attach your test script as that will help us to reproduce the issue.
>>>
>>> On Wed, Jan 27, 2016 at 1:21 PM, Junhwan Choi (최준환)
>>> <choi.junhwan at gmail.com> wrote:
>>>> Hi Nathan,
>>>>
>>>> Now I change as you suggested
>>>> ===============================
>>>> import matplotlib as matplotlib
>>>> matplotlib.use('Agg')
>>>> import yt
>>>> import yt.units as units
>>>> import numpy as np
>>>> import matplotlib.pyplot as plt
>>>>
>>>> def _partradiuspc(field, data):
>>>> return data[('all','particle_radius')].in_units('pc')
>>>> yt.add_field('partradiuspc', function=_partradiuspc,
>>>> particle_type=True, units="pc")
>>>>
>>>> index = 45
>>>> Nbin= 100
>>>> rmax = 3000
>>>> ds = yt.load("../DD%04d/DD%04d" % (index,index))
>>>> ds.index
>>>> ad= ds.all_data()
>>>>
>>>> center = ds.find_max(("gas", "density"))[1]
>>>> rmin = max([1.0e-3,2.0*ds.index.get_smallest_dx().in_units('pc')])
>>>>
>>>> sphere = ds.sphere(center, rmax*units.pc)
>>>> bulk_velocity = sphere.quantities['BulkVelocity']()
>>>> sphere.set_field_parameter('bulk_velocity', bulk_velocity)
>>>>
>>>> profile = yt.Profile1D(sphere, 'partradiuspc', Nbin, x_min=rmin,
>>>> x_max=rmax, x_log=True, weight_field=None)
>>>> profile.add_fields(('all', 'particle_angular_momentum_x'))
>>>> profile.add_fields(('all', 'particle_angular_momentum_y'))
>>>> profile.add_fields(('all', 'particle_angular_momentum_z'))
>>>>
>>>> PartAngularMomentum = np.sqrt(profile[('all', 'particle_angular_momentum_x')]**2
>>>> + profile[('all',
>>>> 'particle_angular_momentum_y')]**2
>>>> + profile[('all',
>>>> 'particle_angular_momentum_z')]**2)
>>>>
>>>> plt.plot(profile.x, PartAngularMomentum, label='Total',linestyle="-",color='r')
>>>>
>>>> plt.xlabel('r [pc]')
>>>> plt.ylabel('pang')
>>>> ===================================
>>>> And, I got the following error message
>>>> ………………
>>>> Traceback (most recent call last):
>>>> File "pang.py", line 26, in <module>
>>>> profile = yt.Profile1D(sphere, 'partradiuspc', Nbin, x_min=rmin,
>>>> x_max=rmax, x_log=True, weight_field=None)
>>>> File "/home/jhchoi/common/src/yt/yt/data_objects/profiles.py", line
>>>> 411, in __init__
>>>> self.x_field = data_source._determine_fields(x_field)[0]
>>>> File "/home/jhchoi/common/src/yt/yt/data_objects/data_containers.py",
>>>> line 1001, in _determine_fields
>>>> raise YTFieldNotFound((ftype,fname),self.ds)
>>>> yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all',
>>>> 'partradiuspc')' in DD0045.
>>>>
>>>> If I remove "particle_type=True" in add_field, it works.
>>>> However, I am not sure that removing "particle_type=True" is ther
>>>> right way or not, because the yt document suggest to include it.
>>>>
>>>> Thank you,
>>>> Junhwan
>>>>
>>>>
>>>> On Tue, Jan 26, 2016 at 2:15 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>>>>> Your 'radiuspc' field is a mesh field, but you're trying to compare it
>>>>> with particle fields. Mesh fields and particle fields don't have the
>>>>> same shape, which is why you're getting an error.
>>>>>
>>>>> You may want to use the particle_radius field instead. If you want to
>>>>> create a derived field with different default units, you'll need to
>>>>> specify particle_type=True in your add_field call.
>>>>>
>>>>> -Nathan
>>>>>
>>>>> On Tue, Jan 26, 2016 at 2:12 PM, Junhwan Choi (최준환)
>>>>> <choi.junhwan at gmail.com> wrote:
>>>>>> Hi yt users,
>>>>>>
>>>>>> I try to make a particle angular momentum profile using the following script:
>>>>>> ================================
>>>>>> import matplotlib as matplotlib
>>>>>> matplotlib.use('Agg')
>>>>>> import yt
>>>>>> import yt.units as units
>>>>>> import numpy as np
>>>>>> import matplotlib.pyplot as plt
>>>>>>
>>>>>> def _radiuspc(field, data):
>>>>>> return data[('radius')].in_units('pc')
>>>>>> yt.add_field('radiuspc', function=_radiuspc, units="pc")
>>>>>>
>>>>>> index = 45
>>>>>> Nbin= 100
>>>>>> rmax = 3000
>>>>>> ds = yt.load("../DD%04d/DD%04d" % (index,index))
>>>>>> ds.index
>>>>>> ad= ds.all_data()
>>>>>> center = ds.find_max(("gas", "density"))[1]
>>>>>> rmin = max([1.0e-3,2.0*ds.index.get_smallest_dx().in_units('pc')])
>>>>>>
>>>>>> sphere = ds.sphere(center, rmax*units.pc)
>>>>>> bulk_velocity = sphere.quantities['BulkVelocity']()
>>>>>> sphere.set_field_parameter('bulk_velocity', bulk_velocity)
>>>>>>
>>>>>> profile = yt.Profile1D(sphere, 'radiuspc', Nbin, x_min=rmin,
>>>>>> x_max=rmax, x_log=True, weight_field=None)
>>>>>> profile.add_fields(('all', 'particle_angular_momentum_x'))
>>>>>> profile.add_fields(('all', 'particle_angular_momentum_y'))
>>>>>> profile.add_fields(('all', 'particle_angular_momentum_z'))
>>>>>>
>>>>>> PartAngularMomentum = np.sqrt(profile[('all', 'particle_angular_momentum_x')]**2
>>>>>> + profile[('all',
>>>>>> 'particle_angular_momentum_y')]**2
>>>>>> + profile[('all',
>>>>>> 'particle_angular_momentum_z')]**2)
>>>>>>
>>>>>> plt.plot(profile.x, PartAngularMomentum, label='Total',linestyle="-",color='r')
>>>>>>
>>>>>> plt.xlabel('r [pc]')
>>>>>> plt.ylabel('pang')
>>>>>> ======================================
>>>>>> And I got the following error:
>>>>>> ………..
>>>>>> Traceback (most recent call last):
>>>>>> File "pang.py", line 26, in <module>
>>>>>> profile.add_fields(('all', 'particle_angular_momentum_x'))
>>>>>> File "/home/jhchoi/common/src/yt/yt/data_objects/profiles.py", line
>>>>>> 112, in add_fields
>>>>>> self._bin_chunk(chunk, fields, temp_storage)
>>>>>> File "/home/jhchoi/common/src/yt/yt/data_objects/profiles.py", line
>>>>>> 425, in _bin_chunk
>>>>>> rv = self._get_data(chunk, fields)
>>>>>> File "/home/jhchoi/common/src/yt/yt/data_objects/profiles.py", line
>>>>>> 240, in _get_data
>>>>>> arr[:,i] = chunk[field][filter].in_units(units)
>>>>>> File "/home/jhchoi/common/src/yt/yt/units/yt_array.py", line 1123,
>>>>>> in __getitem__
>>>>>> ret = super(YTArray, self).__getitem__(item)
>>>>>> IndexError: index 1322 is out of bounds for axis 1 with size 1322
>>>>>>
>>>>>> I do not understand what the problem is?
>>>>>>
>>>>>> One more question:
>>>>>> Is there any way to make accumulation density profile with yt.Profile1D(……)?
>>>>>>
>>>>>> Thank you in advance,
>>>>>> Junhwan
>>>>>> _______________________________________________
>>>>>> yt-users mailing list
>>>>>> yt-users at lists.spacepope.org
>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>> _______________________________________________
>>>>> yt-users mailing list
>>>>> yt-users at lists.spacepope.org
>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
More information about the yt-users
mailing list