Mailman 3 - yt-users

Re: [yt-users] yt.extensions.EnzoSimulation gorne
by Elizabeth Tasker 08 Nov '10

08 Nov '10

Actually, it turns out this is still giving me problems. I'm now using yt 2.0 and have: from yt.analysis_modules.api import EnzoSimulation es = EnzoSimulation("SedovBlastAMR.enzo", initial_time=0.0, final_time=0.1) ETot = [] for output in es.allOutputs: pf = load(output['filename']) data = pf.h.all_data() ETot.append(data.quantities["TotalQuantity"]("TotalEnergy")[0]) . . . But I get: IndexError Traceback (most recent call last) /saw_sfs/work/taskere/yt-2/scripts/iyt in <module>() 15 # calculate total energy for the simulation volume 16 data = pf.h.all_data() ---> 17 ETot.append(data.quantities["TotalQuantity"]("TotalEnergy")[0]) 18 19 # calculate the time of output . . . IndexError: index (100) out of range (0<=index<99) in dimension 0 WARNING: Failure executing file: <total_energy.py> What did I do wrong? Elizabeth Elizabeth Tasker wrote: > Hi Jeff, > > I think it might be enzo 1.7, but inspired by your comment I > controversially checked the code and found > > import yt.extensions.enzo_simulation as ES > > works. > > Thanks, Elizabeth > > > j s oishi wrote: >> Hi Elizabeth, >> >> Are you on yt-2.0? If so, then it should be >> >> from yt.analysis_modules.api import EnzoSimulation as ES >> >> j

3 4

Trac is down
by Matthew Turk 05 Nov '10

05 Nov '10

Hi all, Just a quick note that I know that the yt Trac is down. There was a server migration that evidently Trac didn't handle well; I'm going to try to address it as soon as I can, but I'm traveling this week so it may not be until late tonight or tomorrow night. The documentation should still be up. If you're getting host timeouts -- can't access the website -- those should be resolved in a few hours when DNS catches up to the server migration. Sorry about the inconvenience! -Matt

1 0

adapting multi plot - 3 plots
by Elizabeth Harper-Clark 04 Nov '10

04 Nov '10

Hi all, I have adapted the multi plot script from the cookbook an dit all works as long as I only want 2 plot. When I try to increase to three I get: [h-clark@tpb4 my_scripts]$ python2.6 MultiPlot.py GMCsetup3 1.0 0.714285714286 yt INFO 2010-11-04 11:53:30,115 Created plot collection with default plot-center = [0.51190100000000005, 0.45233099999999998, 0.434998] yt INFO 2010-11-04 11:53:30,127 Getting the binary hierarchy yt INFO 2010-11-04 11:53:30,160 Finished with binary hierarchy reading yt INFO 2010-11-04 11:53:30,253 Adding PotentialField to list of fields yt INFO 2010-11-04 11:53:30,254 Adding AccelerationField1 to list of fields yt INFO 2010-11-04 11:53:30,254 Adding HeII_gamma to list of fields yt INFO 2010-11-04 11:53:30,254 Adding RadAccel1 to list of fields yt INFO 2010-11-04 11:53:30,254 Adding RadAccel2 to list of fields yt INFO 2010-11-04 11:53:30,255 Adding RadAccel3 to list of fields yt INFO 2010-11-04 11:53:30,255 Adding HI_kph to list of fields yt INFO 2010-11-04 11:53:30,255 Adding HeII_kph to list of fields yt INFO 2010-11-04 11:53:30,255 Adding HI_gamma to list of fields [0 0 0] yt INFO 2010-11-04 11:53:31,962 Added slice of Density at x = 0.511901 with 'center' = [0.51190100000000005, 0.45233099999999998, 0.434998] yt INFO 2010-11-04 11:53:33,265 Added slice of Temperature at x = 0.511901 with 'center' = [0.51190100000000005, 0.45233099999999998, 0.434998] yt INFO 2010-11-04 11:53:34,933 Added slice of HII_Fraction at x = 0.511901 with 'center' = [0.51190100000000005, 0.45233099999999998, 0.434998] Traceback (most recent call last): File "MultiPlot.py", line 34, in <module> fig.savefig(frame_template % (sys.argv[-1],ax,n)) File "/home/h-clark/YT/lib/python2.6/site-packages/matplotlib/figure.py", line 1032, in savefig self.canvas.print_figure(*args, **kwargs) File "/home/h-clark/YT/lib/python2.6/site-packages/matplotlib/backend_bases.py", line 1476, in print_figure **kwargs) File "/home/h-clark/YT/lib/python2.6/site-packages/matplotlib/backends/backend_agg.py", line 358, in print_png FigureCanvasAgg.draw(self) File "/home/h-clark/YT/lib/python2.6/site-packages/matplotlib/backends/backend_agg.py", line 314, in draw self.figure.draw(self.renderer) File "/home/h-clark/YT/lib/python2.6/site-packages/matplotlib/artist.py", line 46, in draw_wrapper draw(artist, renderer, *args, **kwargs) File "/home/h-clark/YT/lib/python2.6/site-packages/matplotlib/figure.py", line 773, in draw for a in self.axes: a.draw(renderer) File "/home/h-clark/YT/lib/python2.6/site-packages/matplotlib/artist.py", line 46, in draw_wrapper draw(artist, renderer, *args, **kwargs) File "/home/h-clark/YT/lib/python2.6/site-packages/matplotlib/axes.py", line 1701, in draw im.draw(renderer) File "/home/h-clark/YT/lib/python2.6/site-packages/matplotlib/artist.py", line 46, in draw_wrapper draw(artist, renderer, *args, **kwargs) File "/home/h-clark/YT/lib/python2.6/site-packages/matplotlib/image.py", line 237, in draw im = self.make_image(renderer.get_image_magnification()) File "/home/h-clark/YT/lib/python2.6/site-packages/matplotlib/image.py", line 182, in make_image x = self.to_rgba(self._A, self._alpha) File "/home/h-clark/YT/lib/python2.6/site-packages/matplotlib/cm.py", line 167, in to_rgba x = self.cmap(x, alpha=alpha, bytes=bytes) TypeError: 'NoneType' object is not callable *My Script is:* from yt.mods import * import matplotlib.colorbar as cb orient = 'horizontal' frame_template = "aaSN/%s/multiplot_%01i_%04i" centre = (0.511901, 0.452331, 0.434998) ax = 0 ss = 1 n = 134 pf = load("SciNet/%s/DD%04i/data%04i" % (sys.argv[-1],n, n)) fig, axes, colorbars = get_multi_plot( 3, 1, colorbar=orient, bw = 4) pc = PlotCollection(pf, center=centre) p = pc.add_slice("Density", ax, figure = fig, axes = axes[0][0], use_colorbar=False) p.set_cmap("bds_highcontrast") p = pc.add_slice("Temperature", ax, figure=fig, axes=axes[0][1], use_colorbar=False) p.set_cmap("hot") p = pc.add_slice("HII_Fraction", ax, figure=fig, axes=axes[0][2], use_colorbar=False) p.set_cmap("cold") p.set_width(ss, 'pc') for p, cax in zip(pc.plots, colorbars): cbar = cb.Colorbar(cax, p.image, orientation=orient) p.colorbar = cbar p._autoset_label() fig.savefig(frame_template % (sys.argv[-1],ax,n)) What am I missing? many thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

2 4

halo finding on subvolumes
by Stephen Skory 03 Nov '10

03 Nov '10

Hi all, I have just pushed a change to the mercurial repo that should allow halo finding on subvolumes with all three of the finders in yt. Some of you have asked for this, so I hope it's helpful! This is fairly alpha work, so if you want to use it, please use it with caution. Double-check the results to make sure things make sense. I will not be surprised if something doesn't work, so please do let me know if you run into a problem. As far as I can tell, it works in serial and in parallel on subvolumes, which may be handy. Here's a quick example of how to use it. Basically, the subvolume you define needs to be "comfortably" larger than the region over which you which to find halos. "Comfortable" means perhaps 10% larger on each side, but you can experiment with that. If you don't define a 'subvolume', it will default to the full box, which is how the halo finders have behaved all along. Oh, and the region has to be a "region" not a "sphere" or anything non-rectilinear like that. ---- from yt.mods import * from yt.analysis_modules.halo_finding.api import * pf = load('data0458') sv = pf.h.region([0.5]*3, [0.21, .21, .72], [.28, .28, .79]) halos = HaloFinder(pf, subvolume = sv) halos.write_out("sv.out") ---- You use the same "subvolume" construction with the other halo finders. Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

1 0

Re: [yt-users] parallelHOP problem, did I break python?
by Stephen Skory 03 Nov '10

03 Nov '10

Geoffrey, > 4. So can someone point me to a 2.0 installation script? > Thanks a bunch. I think the simplest way to get this is to make a new copy of yt in your src/ directory. Do something like this: $ hg clone http://hg.enzotools.org/yt/ yt-2 and then go into yt-2, and copy the 'hdf5.cfg' file from the yt source you have been using in here. Make sure you're using the correct branch "yt": $ hg branch yt And then do: $ python setup.py install You'll have to "make" the fKDpy.so file again, and then do the command above again. Remember, this is the branch that is under active development and has many changes compared to older versions of yt. Some of your scripts may not work without modification. Good luck! Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

3 5

Re: [yt-users] parallelHOP problem, did I break python?
by Stephen Skory 29 Oct '10

29 Oct '10

Geoffrey, > yes I redownloaded Forthon, and did everything under "Fortran kD Tree Setup" > section. Let's take a step back and make sure of a few things 1. I'm guessing you're using yt 2.0? Judging from your pasted error message, I think this will fail: "yt.utilities.kdtree import create_tree" 2. And to make sure why it is failing, is there "fKDpy.so" in your equivalent to this directory? lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/utilities/kdtree 3. Similarly, is there a .so in your equivalent to this? src/yt-hg/yt/utilities/kdtree 4. I just looked at the pHOP code, and there were a couple missing imports that I fixed and just pushed, but I don't think that caused your error. However, it's worth trying again after updating your installation. Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

2 1

yt.extensions.EnzoSimulation gorne
by Elizabeth Tasker 29 Oct '10

29 Oct '10

Hi, Yt is denying the existence of "yt.extensions.EnzoSimulation ": ImportError Traceback (most recent call last) /home/taskere/yt/src/yt-hg/scripts/iyt in <module>() 2 3 from yt.mods import * ----> 4 import yt.extensions.EnzoSimulation as ES 5 6 ETot = [] ImportError: No module named EnzoSimulation Did it change name? I want to iterate through all outputs: es = ES.EnzoSimulation("SedovBlastAMR.enzo", initial_time=0.0, final_time=0.1) for output in es.allOutputs # do barbaric calculations at all output times etc. Thanks, Elizabeth

2 2

Re: [yt-users] parallelHOP problem, did I break python?
by Stephen Skory 29 Oct '10

29 Oct '10

Geoffrey, > name 'fKD' is not defined did you upgrade your yt? You need to build the fKDpy.so file: http://yt.enzotools.org/doc/extensions/running_halofinder.html#fortran-kd-t… Does that fix it? Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

2 3

add_ray problem
by Elizabeth Tasker 28 Oct '10

28 Oct '10

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

3 5

Particle profiles
by Elizabeth Tasker 26 Oct '10

26 Oct '10

Hi, I'd like to plot dark matter particle density as a function of radius for my particle-only simulation. Can I use add_profile_sphere, but for particles rather than gas? I only have a single halo and I know the halo it's centred in the middle of my box (or it better be, since I put it there!). Is this possible? Thanks, Elizabeth

4 10