<div dir="ltr"><div>Hi again,</div><div><br></div>That did the trick!!!! So there was a small bug with that dictionary I take it. I've been sweating bullets because my advisor wanted me to just use IDL if I couldn't get up and running with yt. And I am so very tired of the wasted hours that accompany IDL scripts!!!<div>
<br></div><div>Many thanks,</div><div>Tim</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Aug 20, 2013 at 11:06 AM, Matthew Turk <span dir="ltr"><<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Tim,<br>
<div class="im"><br>
On Tue, Aug 20, 2013 at 1:03 PM, Timothy Waters<br>
<<a href="mailto:waterst3@unlv.nevada.edu">waterst3@unlv.nevada.edu</a>> wrote:<br>
> Hi Matt,<br>
><br>
> I greatly appreciate the help. The pictures you see are what I get on a<br>
> first run using<br>
> %run scatter3DAthenaData.py<br>
> Whether or not I then close the plot window, issuing %run<br>
> scatter3DAthenaData.py again brings up a new plot with the mess of points.<br>
> So maybe this is just specific to my install? I suppose I should try<br>
> running it on my linux box then.<br>
<br>
</div>It's possible, but I'm not entirely sure yet. There were some recent<br>
changes to Athena, which actually relate to retaining state in between<br>
iterations, so let's have a shot at that first. (There was a<br>
dictionary being put in the class structure which could be mutable in<br>
between iterations.)<br>
<br>
After activating, try:<br>
<br>
cd /Users/Macbook/Virtualenvs/yt/yt-x86_64/src/yt-hg<br>
hg pull -r yt<br>
hg up -C -r yt<br>
python2.7 setup.py build_ext -i -f<br>
<br>
and try running again?<br>
<br>
-Matt<br>
<div class="HOEnZb"><div class="h5"><br>
><br>
> Here is the output of yt instinfo:<br>
> (yt-x86_64)Macbook$ yt instinfo:<br>
> %<br>
> yt module located at:<br>
> /Users/Macbook/Virtualenvs/yt/yt-x86_64/src/yt-hg<br>
> The supplemental repositories are located at:<br>
> /Users/Macbook/Virtualenvs/yt/yt-x86_64/src/yt-supplemental<br>
><br>
> The current version of the code is:<br>
><br>
> ---<br>
> cde0a641f1bf<br>
> ---<br>
><br>
> This installation CAN be automatically updated.<br>
> yt dependencies were last updated on<br>
> Tue Aug 13 16:45:11 PDT 2013<br>
> %<br>
><br>
> Also, here is the output from %run scatter3DAthenaData.py:<br>
><br>
> %<br>
> yt : [INFO ] 2013-08-20 09:59:25,321 Temporarily setting<br>
> domain_right_edge = -domain_left_edge. This will be corrected automatically<br>
> if it is not the case.<br>
> yt : [INFO ] 2013-08-20 09:59:25,323 Parameters: current_time<br>
> = 15.0<br>
> yt : [INFO ] 2013-08-20 09:59:25,323 Parameters: domain_dimensions<br>
> = [32 32 32]<br>
> yt : [INFO ] 2013-08-20 09:59:25,324 Parameters: domain_left_edge<br>
> = [-0.5 -0.5 -0.5]<br>
> yt : [INFO ] 2013-08-20 09:59:25,325 Parameters: domain_right_edge<br>
> = [ 0.5 0.5 0.5]<br>
> yt : [INFO ] 2013-08-20 09:59:25,325 Parameters: cosmological_simulation<br>
> = 0.0<br>
> Nx,Ny,Nz = [40 40 40]<br>
> cell sizes (x,y,z) = [ 0.03125 0.03125 0.03125]<br>
> yt : [INFO ] 2013-08-20 09:59:25,327 Getting field x from 1<br>
> yt : [INFO ] 2013-08-20 09:59:25,345 Getting field y from 1<br>
> yt : [INFO ] 2013-08-20 09:59:25,353 Getting field z from 1<br>
> yt : [INFO ] 2013-08-20 09:59:25,361 Getting field density from 1<br>
> yt : [INFO ] 2013-08-20 09:59:25,370 Getting field momentum_x from 1<br>
> yt : [INFO ] 2013-08-20 09:59:25,381 Getting field momentum_y from 1<br>
> yt : [INFO ] 2013-08-20 09:59:25,389 Getting field momentum_z from 1<br>
> %<br>
><br>
> Thanks again!<br>
><br>
><br>
> On Tue, Aug 20, 2013 at 8:43 AM, Matthew Turk <<a href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>> wrote:<br>
>><br>
>> Hi Tim,<br>
>><br>
>> Thanks for writing, and welcome to yt!<br>
>><br>
>> On Sun, Aug 18, 2013 at 8:53 PM, Timothy Waters<br>
>> <<a href="mailto:waterst3@unlv.nevada.edu">waterst3@unlv.nevada.edu</a>> wrote:<br>
>> > Hi,<br>
>> ><br>
>> > Here is the data and simple script to make a scatter or profile plot of<br>
>> > my<br>
>> > simulation output,<br>
>> > <a href="https://www.dropbox.com/sh/ibpda938ltsxl0j/2AA2FYDUH8#/" target="_blank">https://www.dropbox.com/sh/ibpda938ltsxl0j/2AA2FYDUH8#/</a><br>
>> ><br>
>> > This is a spherically symmetric (cartesian [-0.5,0.5]^3, 32cells^3)<br>
>> > hydro<br>
>> > simulation with initial conditions<br>
>> > density = 1.0 if radius <= 1/3;<br>
>> > density falls off as 1/r^2 if r > 1/3;<br>
>> > velocity is everywhere 0<br>
>> ><br>
>> > The output with these ICs is WP12.0000.vtk. When I run my script the<br>
>> > first<br>
>> > time using iyt I get the first image with the expected ICs. Running it<br>
>> > again gives the second image and I don't know why. I'm hoping those<br>
>> > other<br>
>> > points don't actually exist in my data. Maybe I am just missing<br>
>> > something<br>
>> > simple?<br>
>><br>
>> I'm not sure. I haven't been able to replicate the problem here, but<br>
>> I have a handful of suspicions. I was able to generate these two<br>
>> images, one for the 0000 dataset and the second for 0030.<br>
>><br>
>> <a href="http://i.imgur.com/cxnDVjO.png" target="_blank">http://i.imgur.com/cxnDVjO.png</a><br>
>> <a href="http://i.imgur.com/MPUSQVH.png" target="_blank">http://i.imgur.com/MPUSQVH.png</a><br>
>><br>
>> Can you tell me a bit more specifically how you're running the script?<br>
>> You start up iyt, then do %run , and then %run again? Does it happen<br>
>> if you do:<br>
>><br>
>> %run scatter3DAthenaData.py<br>
>> %run scatter3DAthenaData.py<br>
>><br>
>> and look at the resultant plot? (It does not for me, FWIW.) Does it<br>
>> happen if you do multiple datasets in a row?<br>
>><br>
>> What's the output of:<br>
>><br>
>> yt instinfo<br>
>><br>
>> specifically, the changeset hash it provides.<br>
>><br>
>> ><br>
>> > The evolved data, WP12.0030.vtk, is provided as well. Running this data<br>
>> > 'cleans the slate' so that I can then go back to see the problem with my<br>
>> > initial conditions again. Of course, the problem shows up in this data<br>
>> > too.<br>
>><br>
>> Interesting. I do not believe that there is a problem with your data,<br>
>> but we'll get to the bottom of it!<br>
>><br>
>> Best,<br>
>><br>
>> Matt<br>
>><br>
>> ><br>
>> > Thanks in advance!<br>
>> > Tim<br>
>> ><br>
>> ><br>
>> > _______________________________________________<br>
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>> ><br>
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</div></div></blockquote></div><br></div>