[yt-users] Analyzing DM-only run
kcai at pa.uky.edu
kcai at pa.uky.edu
Fri Mar 12 09:20:05 PST 2010
Hi Matt and Britton,
Thank you both for teaching me how to plot particles in the past.
Now that I got rid of the redundant particles in the initial
conditions, it is desirable to look at the subsequent evolution in
more detail - in particular, the sphere of particles still got
destroyed fairly quickly. So we suspect it is the initial velocity
field that was not set up properly. However, I tried to use
p = pc.add_slice('particle_density_pyx', 0)
p.modify["velocity"]()
but failed (the add_slice part works):
Traceback (most recent call last):
File "DM_plots.py", line 14, in <module>
pc.save("RD0000/Redshift199")
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/PlotCollection.py", line 81, in
save
override=override, force_save=force_save))
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/PlotTypes.py", line 112, in
save_image
self._redraw_image()
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/PlotTypes.py", line 374, in
_redraw_image
self._run_callbacks()
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/PlotTypes.py", line 238, in
_run_callbacks
cb(self)
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/Callbacks.py", line 75, in
__call__
return qcb(plot)
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/Callbacks.py", line 102, in
__call__
plot.data[self.field_x] - self.bv_x,
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 249, in
__getitem__
self.get_data(key)
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 584, in
get_data
if self._generate_field(field):
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 606, in
_generate_field
self.pf.field_info[field].check_available(self)
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/FieldInfoContainer.py", line 267, in
check_available
validator(data)
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/FieldInfoContainer.py", line 365, in
__call__
raise NeedsDataField(doesnt_have)
yt.lagos.FieldInfoContainer.NeedsDataField: (['y-velocity'])
>>> pc.save("RD0000/Redshift199")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/PlotCollection.py", line 81, in
save
override=override, force_save=force_save))
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/PlotTypes.py", line 112, in
save_image
self._redraw_image()
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/PlotTypes.py", line 374, in
_redraw_image
self._run_callbacks()
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/PlotTypes.py", line 238, in
_run_callbacks
cb(self)
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/Callbacks.py", line 75, in
__call__
return qcb(plot)
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/Callbacks.py", line 102, in
__call__
plot.data[self.field_x] - self.bv_x,
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 249, in
__getitem__
self.get_data(key)
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 584, in
get_data
if self._generate_field(field):
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 606, in
_generate_field
self.pf.field_info[field].check_available(self)
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/FieldInfoContainer.py", line 267, in
check_available
validator(data)
File
"/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/FieldInfoContainer.py", line 365, in
__call__
raise NeedsDataField(doesnt_have)
yt.lagos.FieldInfoContainer.NeedsDataField: (['y-velocity'])
and I tried pc.add_slice('ParticleVelocityMagnitude', 0) and got segfault.
Do you have any suggestions?
In addition, how may I smooth the particle density and see more structures?
Thanks a lot,
Kai
Quoting Matthew Turk <matthewturk at gmail.com>:
> Hi Kai,
>
> You're right, good luck.
>
> -MAtt
>
> On Thu, Mar 11, 2010 at 10:42 PM, <kcai at pa.uky.edu> wrote:
>> Hi Matt,
>> Sorry for responding a bit late - I was out for dinner. We got a visitor
>> here...
>>
>> I did find the gdb command you sent me a while ago, but looks like I get
>> the problem fixed already - I found I can not only reset the
>> NumberOfParticles,
>> but also the "size" of the ParticleField[] array. So I set it to be the same
>> as NumberOfParticles. Now: not only I get a perfect sphere of particles with
>> nothing outside initially; and no segfaults with the YT script now. So you
>> are right - it's those redundant array elements which caused the trouble.
>> So it may not be necessary to get a "backtrace" now - don't you think?
>>
>> Thanks,
>> Kai
>>
>> Quoting Matthew Turk <matthewturk at gmail.com>:
>>
>>> Use gdb, get a backtrace. Alternately, get a core dump and a
>>> backtrace off that. If it's really segfaulting, the problem needs to
>>> be debugged that way.
>>>
>>> On Thu, Mar 11, 2010 at 6:00 PM, <kcai at pa.uky.edu> wrote:
>>>>
>>>> Hi Matt,
>>>> Thanks for helping out. Here is what I got (I don't know what is a "gdb
>>>> backtrace"):
>>>>
>>>>> python2.6 -i DM_plots.py
>>>>
>>>> /home/kca223/lib/python2.6/site-packages/IPython/Magic.py:38:
>>>> DeprecationWarning: the sets module is deprecated
>>>> from sets import Set
>>>> yt INFO 2010-03-11 18:34:20,059 Created plot collection
>>>> with
>>>> default plot-center = [0.5, 0.5, 0.5]
>>>> yt INFO 2010-03-11 18:34:20,172 Getting the binary
>>>> hierarchy
>>>> yt INFO 2010-03-11 18:34:20,174 Finished with binary
>>>> hierarchy
>>>> reading
>>>> yt INFO 2010-03-11 18:34:20,285 Getting field
>>>> particle_position_y from 1
>>>> yt INFO 2010-03-11 18:34:20,285 Getting particle_position_y
>>>> using ParticleIO
>>>> yt INFO 2010-03-11 18:34:20,597 Getting field
>>>> particle_position_z from 1
>>>> yt INFO 2010-03-11 18:34:20,597 Getting particle_position_z
>>>> using ParticleIO
>>>> yt INFO 2010-03-11 18:34:21,214 Generating overlap masks
>>>> for
>>>> level 0
>>>> Reading and masking grids 100%
>>>> |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time:
>>>> 00:00:00
>>>> yt INFO 2010-03-11 18:34:21,215 Finished calculating
>>>> overlap.
>>>> Segmentation fault 0 / 0 0% |
>>>>
>>>> And my YT script:
>>>>
>>>> from yt.mods import *
>>>> pf = load("RD0002/RedDump0002", data_style = "enzo_packed_3d")
>>>> pc = PlotCollection(pf, center = [0.5, 0.5, 0.5])
>>>> pc.add_particles(0, 0.5, p_size=1.0)
>>>> pc.add_projection("particle_density_pyx", 0)
>>>> pc.add_projection("particle_density_pyx", 1)
>>>> pc.save("RD0002/Redshift100")
>>>>
>>>> Thanks in advance,
>>>> Kai
>>>>
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