Re: [yt-users] Analyzing DM-only run

Hi Kai, Right now, the velocity vectors only work with the baryon quantities. It might be possible to make a smoothed, cell-based particle velocity field. I'm not sure why your other command segfaulted; can you send me a separate email off list with a backtrace? -Matt On Mar 12, 2010, at 11:20 AM, kcai@pa.uky.edu wrote:

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):

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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-

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']) 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 :

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Hi Kai,

You're right, good luck.

-MAtt

On Thu, Mar 11, 2010 at 10:42 PM, wrote:

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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 :

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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, wrote:

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Hi Matt, Thanks for helping out. Here is what I got (I don't know what is a "gdb backtrace"):

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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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