<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">All you have to do to get mesh construction to run is access the “index” attribute from the dataset:<div class=""><br class=""></div><div class="">ds = yt.load(something)</div><div class="">ds.index</div><div class=""><br class=""></div><div class=""><div><blockquote type="cite" class=""><div class="">On May 20, 2016, at 3:40 PM, Jiang, Yanfei <<a href="mailto:yanfei.jiang@cfa.harvard.edu" class="">yanfei.jiang@cfa.harvard.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi John,<div class=""><br class=""></div><div class=""> I just paste the script. You can replay the filename with the data you have (I forget which file I sent to you before). </div><div class=""><br class=""></div><div class=""> I should say that at minimum, I should do region selection so that the progress bar for mesh construction shows up. Then the memory leaking issue also shows up.</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Fri, May 20, 2016 at 3:25 PM, John Zuhone <span dir="ltr" class=""><<a href="mailto:jzuhone@gmail.com" target="_blank" class="">jzuhone@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Yan-Fei,<div class=""><br class=""></div><div class="">Can you send a script that shows this? </div><div class=""><br class=""></div><div class="">Try pasting the script with <a href="http://paste.yt-project.org/" target="_blank" class="">paste.yt-project.org</a></div><div class=""><br class=""></div><div class="">Best,</div><div class=""><br class=""></div><div class="">John</div><div class=""><div class="h5"><div class=""><br class=""><div class=""><div class=""><blockquote type="cite" class=""><div class="">On May 20, 2016, at 3:24 PM, Jiang, Yanfei <<a href="mailto:yanfei.jiang@cfa.harvard.edu" target="_blank" class="">yanfei.jiang@cfa.harvard.edu</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class="">OK. <div class=""><br class=""></div><div class="">By the way, the memory leaking issue with the new function for Athena++ seems to come from mesh construction. I tried a case with yt just reading the data without any plot, the memory usage still goes up with time. </div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Fri, May 20, 2016 at 3:13 PM, John Zuhone <span dir="ltr" class=""><<a href="mailto:jzuhone@gmail.com" target="_blank" class="">jzuhone@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Hi Yan-Fei,<div class=""><br class=""></div><div class="">And in the athena_pp bookmark I will set this to the default for cylindrical and spherical coordinates instead of “domain” which is what I had it set to. </div><span class=""><font color="#888888" class=""><div class=""><br class=""></div><div class="">John</div></font></span><div class=""><div class=""><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On May 20, 2016, at 3:12 PM, Jiang, Yanfei <<a href="mailto:yanfei.jiang@cfa.harvard.edu" target="_blank" class="">yanfei.jiang@cfa.harvard.edu</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class="">Thank you, Nathan. This indeed is what I need. </div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Fri, May 20, 2016 at 3:09 PM, Nathan Goldbaum <span dir="ltr" class=""><<a href="mailto:nathan12343@gmail.com" target="_blank" class="">nathan12343@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">Hi Yanfei,<div class=""><br class=""></div><div class="">So I looked a little closer at the code. It looks like the 'domain' origin sets the origin of the plot at the lower-left-hand corner of the *domain*, which for your dataset is *not* the same thing as setting the origin of the plot at the origin of the simulation's coordinate system.</div><div class=""><br class=""></div><div class="">What you want is to set the origin to 'native', which sets the origin to be the same as the origin of the simulation coordinate system. Here is an example with that choice:</div><div class=""><br class=""></div><div class=""><a href="https://gist.github.com/e61ac07b44e5083ea88fcf1bf24a3459" target="_blank" class="">https://gist.github.com/e61ac07b44e5083ea88fcf1bf24a3459</a><br class=""></div><div class=""><br class=""></div><div class="">Hope that's helpful,</div><div class=""><br class=""></div><div class="">Nathan</div></div><div class=""><div class=""><div class="gmail_extra"><br class=""><div class="gmail_quote">On Thu, May 19, 2016 at 3:29 PM, Jiang, Yanfei <span dir="ltr" class=""><<a href="mailto:yanfei.jiang@cfa.harvard.edu" target="_blank" class="">yanfei.jiang@cfa.harvard.edu</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">Hi Nathan,<div class=""><br class=""></div><div class=""> Here is a much smaller data file that you can try:</div><div class=""><br class=""></div><div class=""><a href="https://drive.google.com/file/d/0ByTG4wYr-7aOdUxUR0dMWGZVQmM/view?usp=sharing" target="_blank" class="">https://drive.google.com/file/d/0ByTG4wYr-7aOdUxUR0dMWGZVQmM/view?usp=sharing</a><br class=""></div><div class=""><br class=""></div><div class="">Now the inner boundary is 28 and it is labeled as 0. </div><div class=""><br class=""></div></div><div class=""><div class=""><div class="gmail_extra"><br class=""><div class="gmail_quote">On Thu, May 19, 2016 at 3:07 PM, Nathan Goldbaum <span dir="ltr" class=""><<a href="mailto:nathan12343@gmail.com" target="_blank" class="">nathan12343@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">Hi Yanfei,<div class=""><br class=""></div><div class="">John ZuHone gave me access to your dataset - I think the issue is that ds.domain_left_edge is [2, 0, 0], and that is confusing the code that generates the plot coordinates for spherical geometries.</div><div class=""><br class=""></div><div class="">I don't think this is an issue with the frontend, but a general issue with plotting data in spherical coordinates with an inner radial boundary.</div><div class=""><br class=""></div><div class="">I don't have any test datasets besides yours that look like this, and yours is pretty large, so it would be nice to have a smaller dataset to play with.</div><div class=""><br class=""></div><div class="">-Nathan</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote"><div class=""><div class="">On Thu, May 19, 2016 at 10:59 AM, Jiang, Yanfei <span dir="ltr" class=""><<a href="mailto:yanfei.jiang@cfa.harvard.edu" target="_blank" class="">yanfei.jiang@cfa.harvard.edu</a>></span> wrote:<br class=""></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class=""><div class=""><div dir="ltr" class="">Hi,<div class=""><br class=""></div><div class=""> I am trying to make a slice plot with the new capability for spherical polar grid in Athena++ data John developed. The attached notebook.png shows what I am doing. I take a slice and the origin is set to "domain". The image.png is the image from the notebook. In the slice image, the empty space near the center corresponds to the inner radial boundary of the original spherical coordinate, which is 2 in this case. Therefore, I think the x stick where is 0 in the plot should be 2. Do you know any way to fix this?</div><div class=""><br class=""></div><div class="">Thanks. <span class=""><font color="#888888" class=""><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class=""><div dir="ltr" class="">Yan-Fei Jiang<div class=""><br class=""><div class="">Einstein Fellow</div><div class="">Harvard-Smithsonian Center for Astrophysics</div><div class="">60 Garden Street, Cambridge MA USA 02138</div><div class=""></div></div></div></div>
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