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

Timothy Waters waterst3 at unlv.nevada.edu
Tue Aug 20 11:44:47 PDT 2013 

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 <matthewturk at gmail.com>wrote:

> 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
> >> >
> >> >
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