<div dir="ltr">I'm not sure if this is the main cause of the problem, but the units for that simulation should be kpc/h not Mpc/h. It looks like yt is assuming the box is 50,000 Mpc/h on a side. You can set the units in the yt.GadgetDataset command (<a href="http://yt-project.org/doc/examining/loading_data.html?highlight=gadget#units-and-bounding-boxes">http://yt-project.org/doc/examining/loading_data.html?highlight=gadget#units-and-bounding-boxes</a>). Try something like this, <br>
<br><pre><span class="">ds</span> <span class="">=</span> <span class=""><span class="">Gadget</span>Dataset</span><span class="">(</span><span class="">"snap_005"</span><span class="">,</span>
<span class="">unit_base</span> <span class="">=</span> <span class="">{</span><span class="">'length'</span><span class="">:</span> <span class="">(</span><span class="">'kpccm/h'</span><span class="">,</span> <span class="">1.0</span><span class="">)})<br>
<br></span></pre>best, <br>-Gabriel<br><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Aug 8, 2014 at 12:39 PM, Jared Coughlin <span dir="ltr"><<a href="mailto:Jared.W.Coughlin.29@nd.edu" target="_blank">Jared.W.Coughlin.29@nd.edu</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>Thank you for responding! I tried what you suggested, but still no luck. I'm still getting the index out of bounds error. I've copied the traceback to the paste bin at: <a href="http://paste.yt-project.org/show/5001/" target="_blank">http://paste.yt-project.org/show/5001/</a></div>
<div>I've included how I loaded the snapshot as well as the call to yt.SlicePlot, in case that helps. Thank you very much for all the help! </div><span class="HOEnZb"><font color="#888888"><div>-Jared</div></font></span></div>
<div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">
On Thu, Aug 7, 2014 at 5:12 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@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 Jared,<div><br></div><div>Try instead:</div><div><br></div><div>yt.SlicePlot(ds, 'z', ('gas', 'density'), width=(10000., 'kpc'), center ='m')<br></div><div><br></div>
<div>(note the lower-case).</div><div><br></div><div>('Gas', 'Density') is a particle field, i.e. the Density values associated with each of the Gas particles in your simulation. ('gas', 'density') is a mesh field - for SPH it is the smoothed gas density, taken from the original Gas particles. Particle fields are unstructured, the field is only defined at the positions where particles exist. Mesh fields are defined over the whole simulation domain.</div>
<div><br></div><div>Unfortunately there's some name collision here for gadget binary files so I can see how this is confusing. At the very least we should catch that you're trying to create a SlicePlot of a particle field and crash with a nicer, more understandable error.</div>
<div><br></div><div>More detail on the difference between particle and mesh fields as well as fields in yt in general here: <a href="http://yt-project.org/docs/3.0/analyzing/fields.html" target="_blank">http://yt-project.org/docs/3.0/analyzing/fields.html</a></div>
<div><br></div><div>Hope that helps,</div><div><br></div><div>-Nathan</div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div>On Thu, Aug 7, 2014 at 2:08 PM, Jared Coughlin <span dir="ltr"><<a href="mailto:Jared.W.Coughlin.29@nd.edu" target="_blank">Jared.W.Coughlin.29@nd.edu</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr">Hi Nathan, I pasted the traceback here: <a href="http://paste.yt-project.org/show/4998/" target="_blank">http://paste.yt-project.org/show/4998/</a><span><font color="#888888"><div>
-Jared</div></font></span></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div>
On Thu, Aug 7, 2014 at 4:16 PM, Jared Coughlin <span dir="ltr"><<a href="mailto:Jared.W.Coughlin.29@nd.edu" target="_blank">Jared.W.Coughlin.29@nd.edu</a>></span> wrote:<br></div><div><div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hello! I have a vanilla gadget snapshot (one from the lcdm sample run that the code comes with) that I was able to plot by following the instructions given here: <div><a href="http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook" target="_blank">http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook</a><div>
<br></div><div>I then moved on to the 'Making Smoothed Images' section of that page and tried the SlicePlot command. However, I get the following error:</div><div>IndexError: index 32767 is out of bounds for axis 0 with size 32767</div>
<div><br></div><div>Basically, I'm not really sure what that means. It seems like it's overstepping the bounds of an array, as, for a zero-indexed array of size 32767, index 32767 would be out of bounds by one. I just wanted to see if anyone else has had this problem, and if so, how they fixed it? Thank you very much! </div>
<span><font color="#888888">
<div>-Jared </div></font></span></div></div>
</blockquote></div></div></div><br></div>
<br></div></div>_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div><br></div></div>
<br>_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div><br></div>
</div></div><br>_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div><br><br clear="all"><br>-- <br><div dir="ltr">-- <br>Gabriel Altay, PhD<br>Center for Relativistic Astrophysics<br>Georgia Institute of Technology, Physics Department<br>837 State Street, Atlanta, GA, 30332<br>
<div>phone: +01 404 205 9795<br>url: <a href="http://cosmo.gatech.edu/?page_id=1075" target="_blank">http://cosmo.gatech.edu/?page_id=1075</a><br></div></div>
</div>