<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/">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><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 class="HOEnZb"><div class="h5"><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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