Mailman 3 November 2010 - yt-users

Energy Spectrum
by Elizabeth Tasker Nov. 12, 2010

Nov. 12, 2010

Hi, No one has magically already set up a routine in yt / enzo anyl to calculate the energy spectrum of a simulation have they? Elizabeth

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TotalEnergy
by Elizabeth Tasker Nov. 10, 2010

Nov. 10, 2010

Okay, new question: When I call: data.quantities["TotalQuantity"]("TotalEnergy")[0] Is that truly total energy or actually the second baryon field? i.e. when I run yt on a zeus-hydro run will it return the internal energy or the total energy? (I've just run this for a Sedov blast and the total energy seems to be increasing, whereas I was expecting it to drop, since Zeus doesn't perform this test well and looses energy in the first few time-steps). Elizabeth

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library errors?
by Elizabeth Tasker Nov. 10, 2010

Nov. 10, 2010

Hi, I have a yt runtime error: File "/work/taskere/yt/yt-2/lib/python2.6/site-packages/matplotlib/backends/bckend_agg.py", line 221, in _get_agg_font font = FT2Font(str(fname)) RuntimeError: Could not open facefile /home/taskere/yt/lib/python2.6/site-packaes/matplotlib/mpl-data/fonts/ttf/Vera.ttf; Cannot_Open_Resource ... which is not surprising, since home/taskere/yt/lib/python2.6/site-packaes/matplotlib/mpl-data/fonts/ttf/Vera.ttf doesn't exist. There used to be a yt installation at /home/taskere/yt but it's deleted and the version of yt at /work/taskere/yt is a fresh install, so I don't know why it would have linked to a ghost library. Do you have any idea how this might of happened and how I can stop it? Elizabeth

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yt.lagos.AMRRayBase
by gso＠physics.ucsd.edu Nov. 8, 2010

Nov. 8, 2010

I was trying to find the values of a field between two arbitrary points, so instead of ortho_ray which I think is limited to x,y,z, I used "ray" instead. My script worked, but when I tried another set of two points they gave a bunch of errors. I used the following two points: field='Density' end_pt = (0.6015625, 0.1015625, 0.3359375) start_pt = (0.6953125, 0.1015625, 0.6640625) profile = pf.h.ray(start_pt, end_pt, field) it turns out that when part of the the two points are the exactly same (in this case "y" portion) the code would spit out the error at the bottom of this email. is this a bug? I can just change the 0.1015625 to something else that's very similar like 0.1015626 (changing only the last decimal digit) to avoid this error for now, which shouldn't affect my answer too much. From G.S. error: In [187]: profile['t'] yt INFO 2010-11-08 12:32:36,331 Getting field t from 2 --------------------------------------------------------------------------- ZeroDivisionError Traceback (most recent call last) /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-intel.egg/EGG-INFO/scripts/iyt in <module>() ----> 1 2 3 4 5 /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-intel.egg/yt/lagos/BaseDataTypes.pyc in __getitem__(self, key) 247 if key not in self.fields: 248 self.fields.append(key) --> 249 self.get_data(key) 250 return self.data[key] 251 /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-intel.egg/yt/lagos/BaseDataTypes.pyc in get_data(self, fields, in_grids) 422 self[field] = na.concatenate( 423 [self._get_data_from_grid(grid, field) --> 424 for grid in self._grids]) 425 if not self.data.has_key(field): 426 continue /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-intel.egg/yt/lagos/BaseDataTypes.pyc in _get_data_from_grid(self, grid, field) 527 528 def _get_data_from_grid(self, grid, field): --> 529 mask = na.logical_and(self._get_cut_mask(grid), 530 grid.child_mask) 531 if field == 'dts': return self._dts[grid.id][mask] /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-intel.egg/yt/lagos/BaseDataTypes.pyc in check_cache(self, grid) 56 return func(self, grid) 57 elif grid.id not in self._cut_masks: ---> 58 cm = func(self, grid) 59 self._cut_masks[grid.id] = cm 60 return self._cut_masks[grid.id] /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-intel.egg/yt/lagos/BaseDataTypes.pyc in _get_cut_mask(self, grid) 540 from yt.amr_utils import VoxelTraversal 541 VoxelTraversal(mask, ts, dts, grid.LeftEdge, grid.RightEdge, --> 542 grid.dds, self.center, self.vec) 543 self._dts[grid.id] = na.abs(dts) 544 self._ts[grid.id] = na.abs(ts) /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-intel.egg/yt/amr_utils.so in yt.amr_utils.VoxelTraversal (yt/amr_utils.c:9986)() 154 155 --> 156 157 158 ZeroDivisionError: float division

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Re: [yt-users] yt.extensions.EnzoSimulation gorne
by Elizabeth Tasker Nov. 8, 2010

Nov. 8, 2010

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

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Trac is down
by Matthew Turk Nov. 5, 2010

Nov. 5, 2010

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

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adapting multi plot - 3 plots
by Elizabeth Harper-Clark Nov. 4, 2010

Nov. 4, 2010

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

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halo finding on subvolumes
by Stephen Skory Nov. 3, 2010

Nov. 3, 2010

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)

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Re: [yt-users] parallelHOP problem, did I break python?
by Stephen Skory Nov. 3, 2010

Nov. 3, 2010

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)

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