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

Tue Aug 20 11:06:20 PDT 2013

Hi Tim,

On Tue, Aug 20, 2013 at 1:03 PM, Timothy Waters
<waterst3 at unlv.nevada.edu> wrote:
> 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 points.
> 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

>
> 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
> 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 <matthewturk at gmail.com> wrote:
>>
>> Hi Tim,
>>
>> Thanks for writing, and welcome to yt!
>>
>> On Sun, Aug 18, 2013 at 8:53 PM, Timothy Waters
>> <waterst3 at unlv.nevada.edu> wrote:
>> > Hi,
>> >
>> > Here is the data and simple script to make a scatter or profile plot of
>> > 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.
>>
>> >
>> > The evolved data, WP12.0030.vtk, is provided as well.  Running this data
>> > '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
>>
>> >
>> > Thanks in advance!
>> > Tim
>> >
>> >
>> > _______________________________________________
>> > yt-users mailing list
>> > yt-users at lists.spacepope.org
>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>