[yt-users] particle angular momentum profile error and accumulation profile

Nathan Goldbaum nathan12343 at gmail.com
Wed Jan 27 11:54:15 PST 2016 

Oh, no, I just fixed the formatting of the issues. Myself or someone
else will try to get to the bug report sometime soon.

On Wed, Jan 27, 2016 at 1:53 PM, Junhwan Choi (최준환)
<choi.junhwan at gmail.com> wrote:
> 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
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