[yt-users] particle angular momentum profile error and accumulation profile
Junhwan Choi (최준환)
choi.junhwan at gmail.com
Wed Jan 27 11:21:47 PST 2016
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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