Hi Elizabeth, One possible issue is that the non-ortho ray is normalized to having a length in the "t" direction of 1.0; it's solved as a simple line integrated from point A to point B, and the way that's done is just with normalization.. Can you show us the entirety of the plotting script? -Matt On Thu, Oct 28, 2010 at 11:47 AM, Elizabeth Tasker wrote:

Hi,

I've got some (different) problems with add_ray. I have output from the Sedov blast test (so unitless sytems) which is run with a boxsize of 10. I can analyse the results using:

ray = pf.h.ray([5., 5., 5.], [10.,10.,10.], "Density") p = pc.add_ray([5.,5.,5.], [10.,10.,10.], "Density") oray = pf.h.ortho_ray(0, [5., 5.], "Density")

but only ortho_ray gives the correct result, and it's limited to going along the axes.

I've attached the results from the 3 techniques. fig0010.png shows the analytical solution (red line), the ortho_ray solution (green x) and the pf.h.ray solution (blue circles). DD0010_LineQueryPlot shows the results from pc.add_ray.

Does anyone know why this isn't behaving? A slice of the shock confirms it looks nice and spherical.

Elizabeth

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Hi Elizabeth, I think the trouble is that you're comparing the 'x' coordinates, but they won't vary uniformly between the two types of rays. Can you try with "Radius" or "RadiusCode" and see if that improves it? -Matt On Thu, Oct 28, 2010 at 11:58 AM, Elizabeth Tasker wrote:

Hi Matt,

I did think about that, but it looks from the graph DD0010_LineQueryPlot_0_t_Density.png that the peak is a occuring at about 0.5, when it should be at ~0.9 in a box that runs from 0-->1.

I've attached the script.

Elizabeth

Matthew Turk wrote:

...

Hi Elizabeth,

One possible issue is that the non-ortho ray is normalized to having a length in the "t" direction of 1.0; it's solved as a simple line integrated from point A to point B, and the way that's done is just with normalization..  Can you show us the entirety of the plotting script?

-Matt

On Thu, Oct 28, 2010 at 11:47 AM, Elizabeth Tasker wrote:

...

Hi,

I've got some (different) problems with add_ray. I have output from the Sedov blast test (so unitless sytems) which is run with a boxsize of 10. I can analyse the results using:

ray = pf.h.ray([5., 5., 5.], [10.,10.,10.], "Density") p = pc.add_ray([5.,5.,5.], [10.,10.,10.], "Density") oray = pf.h.ortho_ray(0, [5., 5.], "Density")

but only ortho_ray gives the correct result, and it's limited to going along the axes.

I've attached the results from the 3 techniques. fig0010.png shows the analytical solution (red line), the ortho_ray solution (green x) and the pf.h.ray solution (blue circles). DD0010_LineQueryPlot shows the results from pc.add_ray.

Does anyone know why this isn't behaving? A slice of the shock confirms it looks nice and spherical.

Elizabeth

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I was messing with python earlier and now I'm trying to run the parallel hop, and I got this message: (I've installed Forthon with no problem, did a make under yt/extensions/kdtree already) gso:64x64x64 gso$ python parallelHF.py yt INFO 2010-10-28 16:10:21,666 Getting the binary hierarchy yt INFO 2010-10-28 16:10:21,673 Finished with binary hierarchy reading yt INFO 2010-10-28 16:10:21,675 Gathering a field list (this may take a moment.) yt INFO 2010-10-28 16:10:21,684 Adding Emissivity to list of fields yt INFO 2010-10-28 16:10:21,685 Adding Grey_Radiation_Energy to list of fields yt INFO 2010-10-28 16:10:22,002 Getting particle_position_x using ParticleIO yt INFO 2010-10-28 16:10:22,374 Getting ParticleMassMsun using ParticleIO yt INFO 2010-10-28 16:10:22,763 Initializing HOP yt INFO 2010-10-28 16:10:22,764 Getting creation_time using ParticleIO yt INFO 2010-10-28 16:10:23,149 Getting particle_position_y using ParticleIO yt INFO 2010-10-28 16:10:23,528 Getting particle_position_z using ParticleIO yt INFO 2010-10-28 16:10:23,917 Getting particle_index using ParticleIO yt INFO 2010-10-28 16:10:24,576 Distributing padded particles... yt INFO 2010-10-28 16:10:24,616 Building kd tree for 262144 particles... Traceback (most recent call last): File "parallelHF.py", line 16, in <module> rearrange=True, safety=1.5, premerge=True) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-intel.egg/yt/lagos/HaloFinding.py", line 1625, in __init__ threshold=threshold, dm_only=dm_only, rearrange=rearrange, premerge=premerge) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-intel.egg/yt/lagos/HaloFinding.py", line 1123, in __init__ HaloList.__init__(self, data_source, dm_only) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-intel.egg/yt/lagos/HaloFinding.py", line 795, in __init__ self._run_finder() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-intel.egg/yt/lagos/HaloFinding.py", line 1144, in _run_finder self.threshold, rearrange=self.rearrange, premerge=self.premerge) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-intel.egg/yt/lagos/parallelHOP/parallelHOP.py", line 61, in __init__ self._chain_hop() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-intel.egg/yt/lagos/parallelHOP/parallelHOP.py", line 1421, in _chain_hop self._init_kd_tree() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-intel.egg/yt/lagos/parallelHOP/parallelHOP.py", line 338, in _init_kd_tree fKD.dens = na.asfortranarray(na.zeros(self.size, dtype='float64')) NameError: global name 'fKD' is not defined Does anyone else have the same problem? Will reinstallation of YT on my mac fix it? From G.S.