Mailman 3 - yt-users

Error: cannot convert float infinity to integer
by Jean-Claude Passy 08 Apr '10

08 Apr '10

Dear all, I get the following error when trying to plot a radial profile of the density. Does anyone have an idea how to solve this ? Thanks a lot, Jean-Claude ##################################################################################################################### In [42]: ls CommonEnvelope0001 CommonEnvelope0001.configure CommonEnvelope0001.harrays CommonEnvelope0001.taskmap0000 CommonEnvelope0001.boundary CommonEnvelope0001.cpu0000 CommonEnvelope0001.hierarchy CommonEnvelope0001.taskmap0001 CommonEnvelope0001.boundary.hdf CommonEnvelope0001.cpu0001 CommonEnvelope0001.memorymap CommonEnvelope0001.yt In [43]: import yt.raven as R In [44]: import yt.lagos as L In [45]: filen = 'CommonEnvelope0001' In [46]: data = L.EnzoStaticOutput(filen) In [47]: plot_data = R.PlotCollection(data) yt INFO 2010-04-06 15:39:02,963 Created plot collection with default plot-center = [0.4921875, 0.4921875, 0.4921875] In [48]: plot_data.add_profile_sphere(0.5,'1',["Radius", "Density"]) yt INFO 2010-04-06 15:39:56,695 Getting field Radius from 1 yt INFO 2010-04-06 15:39:56,696 Getting field x from 1 yt INFO 2010-04-06 15:39:56,857 Getting field y from 1 yt INFO 2010-04-06 15:39:56,919 Getting field z from 1 yt INFO 2010-04-06 15:39:56,987 Getting field Density from 1 Out[48]: <yt.raven.PlotTypes.Profile1DPlot object at 0x3724d90> In [49]: plot_data.save('DensityProfile', format = 'png') --------------------------------------------------------------------------- OverflowError Traceback (most recent call last) /rpod2/jcpassy/Enzo/enzo/src/yt/scripts/iyt in <module>() ----> 1 2 3 4 5 /rpod2/jcpassy/Enzo/enzo/src/yt/yt/raven/PlotCollection.pyc in save(self, basename, format, override, force_save) 79 fn.append(plot.save_image(basename, \ 80 format=format, submit=self._run_id, ---> 81 override=override, force_save=force_save)) 82 if self.submit: 83 im = plot.im.copy() /rpod2/jcpassy/Enzo/enzo/src/yt/yt/raven/PlotTypes.pyc in save_image(self, prefix, format, submit, override, force_save) 110 *override* will force no filename generation beyond the prefix. 111 """ --> 112 self._redraw_image() 113 if not override: 114 self._generate_prefix(prefix) /rpod2/jcpassy/Enzo/enzo/src/yt/yt/raven/PlotTypes.pyc in _redraw_image(self) 711 func(self.data[self.fields[0]][indices], 712 self.data[self.fields[1]][indices], --> 713 **self.plot_options) 714 self._autoset_label(self.fields[0], self.set_x_label, 'x') 715 self._autoset_label(self.fields[1], self.set_y_label, 'y') /rpod2/jcpassy/yt-x86_64/lib/python2.6/site-packages/matplotlib/axes.pyc in loglog(self, *args, **kwargs) 3566 b = self._hold 3567 self._hold = True # we've already processed the hold -> 3568 l = self.plot(*args, **kwargs) 3569 self._hold = b # restore the hold 3570 /rpod2/jcpassy/yt-x86_64/lib/python2.6/site-packages/matplotlib/axes.pyc in plot(self, *args, **kwargs) 3435 3436 -> 3437 self.autoscale_view(scalex=scalex, scaley=scaley) 3438 return lines 3439 /rpod2/jcpassy/yt-x86_64/lib/python2.6/site-packages/matplotlib/axes.pyc in autoscale_view(self, tight, scalex, scaley) 1625 self.set_xbound(XL) 1626 if scaley and self._autoscaleYon: -> 1627 YL = self.yaxis.get_major_locator().view_limits(y0, y1) 1628 self.set_ybound(YL) 1629 /rpod2/jcpassy/yt-x86_64/lib/python2.6/site-packages/matplotlib/ticker.pyc in view_limits(self, vmin, vmax) 1117 vmin = minpos 1118 -> 1119 if not is_decade(vmin,self._base): vmin = decade_down(vmin,self._base) 1120 if not is_decade(vmax,self._base): vmax = decade_up(vmax,self._base) 1121 /rpod2/jcpassy/yt-x86_64/lib/python2.6/site-packages/matplotlib/ticker.pyc in is_decade(x, base) 1028 def is_decade(x,base=10): 1029 lx = math.log(x)/math.log(base) -> 1030 return lx==int(lx) 1031 1032 class LogLocator(Locator): OverflowError: cannot convert float infinity to integer #####################################################################################################################

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problems loading yt
by Brian O'Shea 06 Apr '10

06 Apr '10

Dear yt-users, I'm having a very peculiar problem, and I wonder if any of you have experienced this. I have been using my desktop machine to make tons of images of some enzo simulations - literally several thousand images at this point - and yt has mysteriously stopped working. I haven't done anything to python, attempted to upgrade yt, or anything like that... It just started throwing errors about 800 images into a script. It seems that I can get this error by simply typing 'python' and then 'from yt.mods import *'. The error message is at the end of this email. If anybody could give me some advice, I'd appreciate it - it seems like it might actually be deeper than simply a yt problem, though. Thanks! --Brian nibbler:/Users/bwoshea/Desktop/CondBubbleSims/spitzer_0_1_cool%python Python 2.5.4 (r254:67917, Dec 23 2008, 14:57:27) [GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> from yt.mods import * Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-2.0dev-py2.5-macosx-10.3-i386.egg/yt/mods.py", line 32, in <module> import yt.lagos as lagos File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-2.0dev-py2.5-macosx-10.3-i386.egg/yt/lagos/__init__.py", line 97, in <module> from OutputTypes import * File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-2.0dev-py2.5-macosx-10.3-i386.egg/yt/lagos/OutputTypes.py", line 37, in <module> _pf_store = ParameterFileStore() File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-2.0dev-py2.5-macosx-10.3-i386.egg/yt/fido/ParameterFileStorage.py", line 73, in __init__ self._records = self.read_db() File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-2.0dev-py2.5-macosx-10.3-i386.egg/yt/fido/ParameterFileStorage.py", line 211, in read_db else: v['last_seen'] = float(v['last_seen']) ValueError: invalid literal for float(): EnzoStaticOutput >>>

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submit your yt movies to the yt video gallery!
by Britton Smith 31 Mar '10

31 Mar '10

Greetings, With the recent addition of a fantastic volume render to yt, people have been creating some amazing visualizations. To showcase some of the wonderful movies that yt users are making, we've set up video gallery here: http://yt.enzotools.org/video_gallery.html Made something great of your own? Submitting it to the gallery is easy. First, get a free account on vimeo.com. Free accounts will allow you to upload 500 Mb per week. Next, join the yt group on vimeo.com: http://vimeo.com/groups/34915 When you upload your video and add it to the yt group, it will automatically be added to the yt video gallery. And that's it! We look forward to seeing what everyone is up to! Britton Smith, on behalf of the yt hive-mind.

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Ray casting in simple volume rendering
by Nicholas M. Earl 31 Mar '10

31 Mar '10

Hey again YT community, I was hoping to get some heading on using the simple volume rending script that is written up in the YT cookbook, but it seems that direct_ray_casting isn't a part of yt extensions anymore? Is there something to substitute this? I see that in the software sample script, there is a referencing of VolumeRendering, can I use this? Thanks for your time and effort! Nicholas Earl

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saving files with a different resolution
by Luigi Iapichino 31 Mar '10

31 Mar '10

Dear all, in one of my scripts I have something like this: pc = PlotCollection(pf, center=[0.5,0.5,0.5]) p = pc.add_projection("Temperature", 0, weight_field="Density") p.modify["contour"]("Density", ncont=5, take_log=True) ... ... ... pc.save("%s_temp-proj" % pf,override=True) The saved file has a resolution of 800x800. Is there a way to change this number in YT? I had a look in the PlotCollection class, but I haven't found what I'm searching. Looking forward to your suggestions, Cheers Luigi -- --------------------------------------------------------------- Luigi Iapichino Zentrum fuer Astronomie der Universitaet Heidelberg Institut fuer Theoretische Astrophysik Albert-Ueberle-Str. 2, D-69120 Heidelberg, Germany Tel: +49 6221 548983, Fax: +49 6221 544221 e-mail: luigi(a)ita.uni-heidelberg.de URL: http://www.ita.uni-heidelberg.de/~luigi/

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Labels on plot
by Agarwal, Shankar 31 Mar '10

31 Mar '10

Hi, http://drop.io/Dark_Matter_Density In the above plot, the label is Dark_Matter_Density. But the "M" in matter and "D" in Density do not print correctly. How can I correct "M" and "D" ? Here is the script I am using... from yt.mods import * fn = "RedshiftOutput0001" pf = load(fn) reg = pf.h.region([0.5, 0.5, 0.5], [0.45, 0.0, 0.0], [0.55, 1.0, 1.0]) pf.h.save_object(reg, "region") reg1 = pf.h.load_object("region") pc = PlotCollection(pf,center=[0.5, 0.5, 0.5]) p = pc.add_projection("Dark_Matter_Density", 0, source=reg1) p.set_zlim(1e-8, 5e-3) pc.save("%s" % pf) Shankar

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Data over y-axis of x position
by Nicholas Earl 29 Mar '10

29 Mar '10

Hey YT community, I was wondering if anyone had any sort of starting notion for a problem that I face. I've done slices of a wave progressing in the x-y plane (the wave front moves in the x-direction, from x = 0), what I want to do is take the data from one specific x-value (i.e. a strip running the bounds of y at some position x). I wanted to be able to plot the data -- for instance, density -- (ideally, for my situation, it should be some sort of sinusoidal plot) with density as the y axis and y position as the x-axis. Is there anyway I could form this using YT? Thanks for all your time and effort! Nicholas Earl

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DM particles or baryon density field ?
by Agarwal, Shankar 23 Mar '10

23 Mar '10

Hi, The projection, slice, velocity and overplot particles routines: They read the DM particles or gas ? Looking at the density legend, it looks like this is baryon density field. Is there a provision to plot projection and slice for DM ? Also, I get this error when overplotting particles... yt INFO 2010-03-22 12:17:44,051 Created plot collection with default plot-center = [0.5, 0.5, 0.5] yt INFO 2010-03-22 12:17:44,144 Getting the binary hierarchy yt INFO 2010-03-22 12:17:44,153 Finished with binary hierarchy reading yt INFO 2010-03-22 12:17:46,108 Added slice of Density at x = 0.5 with 'center' = [0.5, 0.5, 0.5] Traceback (most recent call last): File "slice.py", line 42, in <module> p.modify["nparticles"](0.005) File "/autohome/u118/agarwa23/yt-x86_64/src/yt-1.6/yt/raven/PlotTypes.py", line 52, in __getitem__ raise KeyError(item) KeyError: 'nparticles' Shankar

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Enzo Users' Workshop - June 28-30, 2010 (San Diego, CA)
by Matthew Turk 22 Mar '10

22 Mar '10

Dear Colleague, Please pass this email along to any researchers that you feel may be interested, and apologies if you receive multiple copies of this message. The Enzo development consortium is pleased to announce the first Enzo Users Workshop, which will take place at the San Diego Supercomputer Center on June 28-30, 2010. This workshop will be take place shortly after the release of Enzo 1.6, which will have several new features (including MHD and radiation transport), and will be targeted at both new and experienced Enzo users. We will present tutorials on both beginning and advanced Enzo subjects, including running existing simulation types, developing new problem initialization routines, and data analysis and visualization using the 'yt' analysis package. Several experienced Enzo users and developers will be available to help users with both beginning and advanced questions. The website for the workshop is http://lca.ucsd.edu/workshops/enzo2010 , which contains a mailing list sign up, draft schedule, and accommodation details. We will be able to partially defray accommodation costs for attending students. We hope to see you there! Sincerely, Matthew Turk, Michael Norman, and Brian O'Shea (on behalf of the Enzo development team)

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Changes to trunk: Volume Rendering, Gadget & Chombo
by Matthew Turk 17 Mar '10

17 Mar '10

Hi all, I've backported to trunk (r1664 & r1665) a bunch of the changes to the volume rendering that have been going on in the mercurial repository. If you're running on yt-1.6 (the stable branch) you can safely ignore the rest of this message. Recall that "yt instinfo" may be able to auto-upgrade your installation! The full set of changes, from my SVN commits, is here: * Updates to the time series code. It's now just about usable. * Adding package parallel_tools, where we will be adding all NEW parallel support code and migrating old code over to. * Ray casting now works in parallel and with non-equal width/height values for the output image. This necessitated a change in API. * Added AMRInclinedBox data object. * Heaviside function added to transfer functions. * VolumeRendering is now an object. direct_ray_cast is now gone. * Added Sam Skillman's image_handling module. * Added HomogenizedBrickCollection and DistributedObjectCollection. These were designed to parallelize the brick partitioning, but I believe we need a new mechanism for that, so currently they do things but not 3D domain decomp. * Adding preliminary support for both Chombo and Gadget. * Vertex-centering is a tiny bit faster. The big things to note are that we have support for very small gadget datasets, in a very limited fashion. If you're interested in helping out with this, let me know. Additionally, Jeff Oishi has added basic support for Chombo datasets. The biggest changes here are that the volume rendering has had a shift in API -- this was to accommodate the fact that it is now parallel. Previously, direct_ray_cast was to be called; now, the object itself hangs off the hierarchy, like all other first-class objects in yt. Where previously, one would import volume_rendering and then call direct_ray_cast, now one would do something like this: -- import yt.extensions.volume_rendering as vr pf = load("DataDump0155.dir/DataDump0155") W = 100.0/pf['au'] SIZE = 1024 c = pf.h.find_max("Density") tf = vr.ColorTransferFunction((-14.0, -10.0)) tf.add_layers(8) # sample a colormap 8 times vp = pf.h.volume_rendering(L, W, c, (SIZE, SIZE), tf) vp.ray_cast() vr.plot_rgb(vp.image, "my_image") -- This would plot a 100 AU wide image, centered at the most dense point, that's 1024x1024. One of the side effects of this change in API is that this exact operation will now operate in parallel. Britton and Sam have reported good scaling for the parallelism; I'm testing it out myself on huge datasets, so hopefully I'll have some benchmarks in the near future. Sorry about the breakage, but I think it's worth it. The "yt instinfo -u" command will attempt to upgrade your current installation, if you're interested in any of these changes. Let us know if this has caused any breakages! Best, Matt

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