<div dir="ltr">Hi Sam,<div><br></div><div>Thanks for the tips. Unfortunately, I sat down this afternoon to implement this fix, but it doesn't seem to help at all. Here's what I tried, in diff format:</div><div><br>
</div><div><a href="http://paste.yt-project.org/show/4377/">http://paste.yt-project.org/show/4377/</a><br></div><div><br></div><div>I also moved the launching plane 2 root grid cells away from the left edge of the grid. I get exactly the same results. I wasn't quite sure from reading the code how many ghost cells the code uses to construct the vertex data; I assumed it only uses one. Thus, I would think moving the launch point 2 cells away from the edge would alleviate the problem if it were a vertex centering issue.</div>
<div><br></div><div>Do you have any further suggestions? </div><div><br></div><div>thanks,</div><div><br></div><div>Jeff</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Mar 11, 2014 at 1:14 AM, Sam Skillman <span dir="ltr"><<a href="mailto:samskillman@gmail.com" target="_blank">samskillman@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 Jeff,<div><br></div><div>(Offline we went back and forth a bit, I think what we came to was probably right. I just want to follow up here.)</div>
<div><br></div><div>The issue seems to be that during the construction of vertex-centered data, the periodicity of the fields are assumed, and the streamlines go nuts. The ideal fix is to get non-periodic vertex-centered data working, but that might take a bit. The quick fix/hack is to modify either the get_vertex_centered_data function in yt/data_objects/grid_patch.py or the logic in _integrate_through_brick in yt/visualization/streamlines.py. You could cut off the integration when it gets close to dx away from the left/right domain edges.</div>
<div><br></div><div>Sorry this was buried, we should probably raise some sort of warning if the simulation data is not periodic.</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>Sam</div></font></span></div>
<div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">
On Fri, Mar 7, 2014 at 3:19 PM, j s oishi <span dir="ltr"><<a href="mailto:jsoishi@gmail.com" target="_blank">jsoishi@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 Sam,<div><br></div><div>Nope, that gives identical results. Any other thoughts?</div><span><font color="#888888"><div><br></div><div>j</div></font></span></div><div><div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Mar 7, 2014 at 5:15 PM, Sam Skillman <span dir="ltr"><<a href="mailto:samskillman@gmail.com" target="_blank">samskillman@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 Jeff,<div><br></div><div>After integrate_trhough_volume, can you call:</div><div>streamlines.clean_streamlines()</div>
<div><br></div><div>In reading this function, I think it will fail since with it complaining about not having a .magnitudes, so perhaps first edit that function to take out the references to self.magnitudes? </div>
<div><br></div><div>The reason I suggest this is that I don't see where in your script it goes through and cleans up the ones that left the domain. </div><div><br></div><div>If that doesn't help, let me know and I'll dive further in to this.</div>
<div><br></div><div>Sorry for the hassle,</div><div>Sam</div>
<div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div>On Fri, Mar 7, 2014 at 1:34 PM, j s oishi <span dir="ltr"><<a href="mailto:jsoishi@gmail.com" target="_blank">jsoishi@gmail.com</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 All (especially Sam),<div><br></div><div>I'm trying to understand some behavior in the streamlines that I don't completely understand. I've documented the problem in a notebook here:</div>
<div>
<br></div><div><a href="https://hub.yt-project.org/nb/2tmwor" target="_blank">https://hub.yt-project.org/nb/2tmwor</a><br></div><div><br></div><div>The notebook has a full statement of the problem. In essense, I'm not sure I understand why streams that I believe should terminate instantly upon launch (because they should walk directly out of the box) have thousands of elements in them (instead of one). I assume there are one or more misconceptions in my understanding, and I'd really welcome any suggestions. </div>
<div><br></div><div>thanks,</div><div><br></div><div>Jeff</div></div>
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