[yt-users] particle angular momentum profile error and accumulation profile
Nathan Goldbaum
nathan12343 at gmail.com
Wed Jan 27 11:23:20 PST 2016
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
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