<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Hi Mikhail,</div><div id="AppleMailSignature"><br></div><div id="AppleMailSignature">Sorry you're having trouble--any chance you can post your script using <a href="http://paste.yt-project.org">paste.yt-project.org</a> or a similar paste service? It'll be easier to figure out what's going on then.</div><div id="AppleMailSignature"><br></div><div id="AppleMailSignature">By the way, what are your simulation's boundary conditions?</div><div id="AppleMailSignature"><br></div><div id="AppleMailSignature">Best,</div><div id="AppleMailSignature"><br></div><div id="AppleMailSignature">John Z<br><br><span style="font-size: 13pt; background-color: rgba(255, 255, 255, 0);">John ZuHone</span><br><div><span style="background-color: rgba(255, 255, 255, 0);">Kavli Center for Astrophysics and Space Research<br>Massachusetts Institute of Technology<br><a href="x-apple-data-detectors://0" x-apple-data-detectors="true" x-apple-data-detectors-type="address" x-apple-data-detectors-result="0">77 Massachusetts Ave.</a>, 37-582G<br><a href="x-apple-data-detectors://1/0" x-apple-data-detectors="true" x-apple-data-detectors-type="address" x-apple-data-detectors-result="1/0">Cambridge, MA 02139</a><br>(w) <a href="tel:617-253-2354" x-apple-data-detectors="true" x-apple-data-detectors-type="telephone" x-apple-data-detectors-result="1/1">617-253-2354</a><br>(m) <a href="tel:781-708-5004" x-apple-data-detectors="true" x-apple-data-detectors-type="telephone" x-apple-data-detectors-result="1/2">781-708-5004</a><br><a href="mailto:jzuhone@space.mit.edu" x-apple-data-detectors="true" x-apple-data-detectors-type="link" x-apple-data-detectors-result="1/3">jzuhone@space.mit.edu</a><br><a href="mailto:jzuhone@gmail.com" x-apple-data-detectors="true" x-apple-data-detectors-type="link" x-apple-data-detectors-result="2">jzuhone@gmail.com</a><br><a href="http://www.jzuhone.com/" x-apple-data-detectors="true" x-apple-data-detectors-type="link" x-apple-data-detectors-result="3">http://www.jzuhone.com</a></span><br style="font-family: UICTFontTextStyleBody; -webkit-text-size-adjust: auto;"></div></div><div><br>On Jul 30, 2015, at 9:30 PM, Mikhail Klassen <<a href="mailto:klassm@mcmaster.ca">klassm@mcmaster.ca</a>> wrote:<br><br></div><blockquote type="cite"><div><div dir="ltr"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">I'm trying to plot 3D streamlines from a FLASH (v.4) dataset. I've based my streamlines script off the version presented on the <a href="http://yt-project.org">yt-project.org</a> website.</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">I consistently get an error about going up the ghost cells in my volume. The error message is:</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><br></div><div class="gmail_default"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><font face="arial, helvetica, sans-serif">RuntimeError: Error: yt attempted to read outside the boundaries of a non-periodic domain along dimension 0.<br></font><font face="arial, helvetica, sans-serif">Region left edge = -3e+18 code_length, Region right edge = 4.5e+18 code_length<br></font><font face="arial, helvetica, sans-serif">Dataset left edge = 0.0 code_length, Dataset right edge = 1.2e+19 code_length</font><font face="arial, helvetica, sans-serif"><br></font><font face="arial, helvetica, sans-serif">This commonly happens when trying to compute ghost cells up to the domain boundary. Two possible solutions are to load a smaller region that does not border the edge or override the periodicity for this dataset.</font></blockquote><div><br></div><div>My FLASH datasets have x/y/zmin = 0.0 and x/y/zmax 1.2e19 cm.</div><div><br></div><div>I seems like yt is trying to read outside my domain, or is bumping up against the guardcells and I have no idea how to prevent it from doing this. I have tried inspecting the code for an obvious solution. A very similar error shows up when I try to make 1D profiles of the entire dataset (dd = ds.all_data()).</div><div><br></div><div>is it possible that yt doesn't support volumes where the (0,0,0) coordinate is a corner of the volume? Any easy solution to the above issue?</div><div><br></div><div>Thanks,</div><div>Mikhail</div></div></div>
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