Trouble plotting 1D scatter data from 3D Athena vtk data.
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? 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. Thanks in advance! Tim
Hi Tim, Thanks for writing, and welcome to yt! On Sun, Aug 18, 2013 at 8:53 PM, Timothy Waters <waterst3@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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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. 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@gmail.com> wrote:
Hi Tim,
Thanks for writing, and welcome to yt!
On Sun, Aug 18, 2013 at 8:53 PM, Timothy Waters <waterst3@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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Hi Tim, On Tue, Aug 20, 2013 at 1:03 PM, Timothy Waters <waterst3@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@gmail.com> wrote:
Hi Tim,
Thanks for writing, and welcome to yt!
On Sun, Aug 18, 2013 at 8:53 PM, Timothy Waters <waterst3@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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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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@gmail.com>wrote:
Hi Tim,
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 <waterst3@unlv.nevada.edu> wrote: 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@gmail.com> wrote:
Hi Tim,
Thanks for writing, and welcome to yt!
On Sun, Aug 18, 2013 at 8:53 PM, Timothy Waters <waterst3@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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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On Tue, Aug 20, 2013 at 2:44 PM, Timothy Waters <waterst3@unlv.nevada.edu> wrote:
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!!!
Oh, awesome! That's great to hear. :) As a quick note, this bug was discovered in the process of adding answer testing for Athena; Athena has been a pretty active area of development, especially thanks to John ZuHone, Sam Skillman and Nathan Goldbaum. If you run into any other problems, let us know! -Matt
Many thanks, Tim
On Tue, Aug 20, 2013 at 11:06 AM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Tim,
On Tue, Aug 20, 2013 at 1:03 PM, Timothy Waters <waterst3@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@gmail.com> wrote:
Hi Tim,
Thanks for writing, and welcome to yt!
On Sun, Aug 18, 2013 at 8:53 PM, Timothy Waters <waterst3@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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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participants (2)
-
Matthew Turk -
Timothy Waters