Re: [yt-users] Trouble plotting 1D scatter data from 3D Athena vtk data.

Hi again, 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!!! Many thanks, Tim On Tue, Aug 20, 2013 at 11:06 AM, Matthew Turk wrote:

Hi Tim,

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Hi Matt,

I greatly appreciate the help. The pictures you see are what I get on a first run using %run scatter3DAthenaData.py Whether or not I then close the plot window, issuing %run scatter3DAthenaData.py again brings up a new plot with the mess of

On Tue, Aug 20, 2013 at 1:03 PM, Timothy Waters wrote: points.

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So maybe this is just specific to my install? I suppose I should try running it on my linux box then.

It's possible, but I'm not entirely sure yet. There were some recent changes to Athena, which actually relate to retaining state in between iterations, so let's have a shot at that first. (There was a dictionary being put in the class structure which could be mutable in between iterations.)

After activating, try:

cd /Users/Macbook/Virtualenvs/yt/yt-x86_64/src/yt-hg hg pull -r yt hg up -C -r yt python2.7 setup.py build_ext -i -f

and try running again?

-Matt

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Here is the output of yt instinfo: (yt-x86_64)Macbook$ yt instinfo: % yt module located at: /Users/Macbook/Virtualenvs/yt/yt-x86_64/src/yt-hg The supplemental repositories are located at: /Users/Macbook/Virtualenvs/yt/yt-x86_64/src/yt-supplemental

The current version of the code is:

--- cde0a641f1bf ---

This installation CAN be automatically updated. yt dependencies were last updated on Tue Aug 13 16:45:11 PDT 2013 %

Also, here is the output from %run scatter3DAthenaData.py:

% yt : [INFO ] 2013-08-20 09:59:25,321 Temporarily setting domain_right_edge = -domain_left_edge. This will be corrected

automatically

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if it is not the case. yt : [INFO ] 2013-08-20 09:59:25,323 Parameters: current_time = 15.0 yt : [INFO ] 2013-08-20 09:59:25,323 Parameters: domain_dimensions = [32 32 32] yt : [INFO ] 2013-08-20 09:59:25,324 Parameters: domain_left_edge = [-0.5 -0.5 -0.5] yt : [INFO ] 2013-08-20 09:59:25,325 Parameters: domain_right_edge = [ 0.5 0.5 0.5] yt : [INFO ] 2013-08-20 09:59:25,325 Parameters: cosmological_simulation = 0.0 Nx,Ny,Nz = [40 40 40] cell sizes (x,y,z) = [ 0.03125 0.03125 0.03125] yt : [INFO ] 2013-08-20 09:59:25,327 Getting field x from 1 yt : [INFO ] 2013-08-20 09:59:25,345 Getting field y from 1 yt : [INFO ] 2013-08-20 09:59:25,353 Getting field z from 1 yt : [INFO ] 2013-08-20 09:59:25,361 Getting field density from 1 yt : [INFO ] 2013-08-20 09:59:25,370 Getting field momentum_x from 1 yt : [INFO ] 2013-08-20 09:59:25,381 Getting field momentum_y from 1 yt : [INFO ] 2013-08-20 09:59:25,389 Getting field momentum_z from 1 %

Thanks again!

On Tue, Aug 20, 2013 at 8:43 AM, Matthew Turk wrote:

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Hi Tim,

Thanks for writing, and welcome to yt!

On Sun, Aug 18, 2013 at 8:53 PM, Timothy Waters wrote:

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Hi,

Here is the data and simple script to make a scatter or profile plot

of

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my simulation output, https://www.dropbox.com/sh/ibpda938ltsxl0j/2AA2FYDUH8#/

This is a spherically symmetric (cartesian [-0.5,0.5]^3, 32cells^3) hydro simulation with initial conditions density = 1.0 if radius <= 1/3; density falls off as 1/r^2 if r > 1/3; velocity is everywhere 0

The output with these ICs is WP12.0000.vtk. When I run my script the first time using iyt I get the first image with the expected ICs. Running it again gives the second image and I don't know why. I'm hoping those other points don't actually exist in my data. Maybe I am just missing something simple?

I'm not sure. I haven't been able to replicate the problem here, but I have a handful of suspicions. I was able to generate these two images, one for the 0000 dataset and the second for 0030.

http://i.imgur.com/cxnDVjO.png http://i.imgur.com/MPUSQVH.png

Can you tell me a bit more specifically how you're running the script? You start up iyt, then do %run , and then %run again? Does it happen if you do:

%run scatter3DAthenaData.py %run scatter3DAthenaData.py

and look at the resultant plot? (It does not for me, FWIW.) Does it happen if you do multiple datasets in a row?

What's the output of:

yt instinfo

specifically, the changeset hash it provides.

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The evolved data, WP12.0030.vtk, is provided as well. Running this

data

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'cleans the slate' so that I can then go back to see the problem with my initial conditions again. Of course, the problem shows up in this data too.

Interesting. I do not believe that there is a problem with your data, but we'll get to the bottom of it!

Best,

Matt

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Thanks in advance! Tim

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