[yt-users] particle angular momentum profile error and accumulation profile
Junhwan Choi (최준환)
choi.junhwan at gmail.com
Wed Jan 27 11:39:36 PST 2016
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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