<div dir="ltr">It is<div><br></div><div><div>yt module located at:</div><div> /Users/semyeong/miniconda2/envs/yt/lib/python2.7/site-packages</div><div><br></div><div>The current version and changeset for the code is:</div><div><br></div><div>---</div><div>Version = 3.2.3</div><div>Changeset = None</div><div>---</div></div><div><br></div><div>Semyeong</div></div><br><div class="gmail_quote"><div dir="ltr">On Tue, May 3, 2016 at 12:09 PM Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com">nathan12343@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Semyeong,<div><br></div><div>I'm not able to reproduce this behavior in yt 3.3dev. Any chance you can share what yt version you're using? The output of "yt version", run from the command line, should be sufficient.</div></div><div dir="ltr"><div><br></div><div>-Nathan</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 3, 2016 at 11:06 AM, Semyeong Oh <span dir="ltr"><<a href="mailto:semyeong.oh@gmail.com" target="_blank">semyeong.oh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Sure, this is the link <a href="http://use.yt/upload/28d51f76" target="_blank">http://use.yt/upload/28d51f76</a><span><font color="#888888"><div><br></div><div>Semyeong</div></font></span></div><div><div><br><div class="gmail_quote"><div dir="ltr">On Tue, May 3, 2016 at 12:05 PM Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Any chance you can link to the HDF5 file? I don't have a gadget development environment set up.<div><br></div><div>You can use the yt curldrop:</div><div><br></div><div>$ curl -T <span style="font-size:12.8px">snapshot_000.hdf5 <a href="http://use.yt/upload/" target="_blank">http://use.yt/upload/</a></span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">And then share the link this prints out here.</span></div></div><div dir="ltr"><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">-Nathan</span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 3, 2016 at 11:02 AM, Semyeong Oh <span dir="ltr"><<a href="mailto:semyeong.oh@gmail.com" target="_blank">semyeong.oh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Nathan,<div><br></div><div>The dataset is just from <a href="http://wwwmpa.mpa-garching.mpg.de/gadget/gadget-2.0.7.tar.gz" target="_blank">http://wwwmpa.mpa-garching.mpg.de/gadget/gadget-2.0.7.tar.gz</a> ICs/gassphere_littleendian.dat, and output from running the simulation (using /Gadget2/parameterfiles/gassphere.{Makefile/param} with format=2 (hdf5)</div><div><br></div><div>Semyeong</div></div><div><div><br><div class="gmail_quote"><div dir="ltr">On Tue, May 3, 2016 at 11:54 AM Matthew Turk <<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Semyeong,<div><br></div><div>Looks like the bounding box is getting confused somehow, and it's seeing it as the same value for left/right edge. I think your ordering of the bbox is correct (if it weren't, then changing the ordering to be [[-bbox_lim, -bbox_lim, -bbox_lim], [bbox_lim, bbox_lim, bbox_lim]] would fix it) but I'm not sure why it's failing.</div></div><div class="gmail_extra"><br><div class="gmail_quote"></div></div><div class="gmail_extra"><div class="gmail_quote">On Tue, May 3, 2016 at 10:46 AM, Semyeong Oh <span dir="ltr"><<a href="mailto:semyeong.oh@gmail.com" target="_blank">semyeong.oh@gmail.com</a>></span> wrote:<br></div></div><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello,<div><br></div><div>I'm having trouble reading gadget-2 both binary and hdf5 format, and</div><div>was wondering if I could get some help.</div><div>I'm testing out with the example distributed with gadget code, the gas sphere example which only</div><div>contains ~1500 gas particles.</div><div><br></div><div>- If I try to read the initial condition (distributed with gadget) binary file with yt.load, this command seems to</div><div>execute fine, but the field_list returns empty list.</div><div><br></div><div>- If I try to read the output of the simulation in hdf5 format,</div><div><div>fname = 'output/snapshot_000.hdf5'</div><div>unit_base = {'UnitLength_in_cm' : 1.,</div><div> 'UnitMass_in_g' : 1.,</div><div> 'UnitVelocity_in_cm_per_s' : 1.}</div><div><br></div><div>bbox_lim = 5</div><div>bbox = [[-bbox_lim,bbox_lim],</div><div> [-bbox_lim,bbox_lim],</div><div> [-bbox_lim,bbox_lim]]</div><div> </div><div>ds = yt.load(fname,unit_base=unit_base, bounding_box=bbox)</div></div><div><br></div><div>and try ds.field_list or ds.print_stats,</div><div>I end up getting something like this <a href="https://gist.github.com/smoh/7779e9ef546f9b05565aef86893dccd2" target="_blank">https://gist.github.com/smoh/7779e9ef546f9b05565aef86893dccd2</a></div><div>which is obscure.</div><div><br></div><div>What am I doing wrong?</div><div><br></div><div>Thanks,</div><div>Semyeong</div></div><span><font color="#888888"><div dir="ltr">-- <br></div><div dir="ltr">Semyeong</div>
</font></span><br></blockquote></div></div><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">_______________________________________________<br>
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</blockquote></div><div dir="ltr">-- <br></div><div dir="ltr">Semyeong</div>