[yt-users] Rendering Volume of FLASH file

Suoqing JI suoqing at physics.ucsb.edu
Fri May 29 23:59:09 PDT 2015


Hi Kilian,

Are you using exactly the same script from the cookbook? I noticed that the domain of your dataset is quite large:

> yt : [INFO     ] 2015-05-29 20:51:30,332 Parameters: domain_left_edge          = [ -2.20000000e+25  -2.20000000e+25  -2.20000000e+25]
> yt : [INFO     ] 2015-05-29 20:51:30,332 Parameters: domain_right_edge         = [  2.20000000e+25   2.20000000e+25   2.20000000e+25]

So I suggest to change the width “w" to be larger or comparable to your domain size, say, 5.e25:

# Set the width of the image.
# Decreasing or increasing this value
# results in a zoom in or out.
W = 1.0

Best wishes,
--
Suoqing JI
Ph.D Student
Department of Physics
University of California, Santa Barbara
http://web.physics.ucsb.edu/~suoqing

> On May 29, 2015, at 12:19 PM, Kilian Gärtner <kilian.gaertner at st.ovgu.de> wrote:
> 
> Hi,
> 
> I want to render a Volume Plot based on data from a FLASH file, which uses HDF5 file format. I tried the tutorial at http://yt-project.org/doc/cookbook/simple_plots.html#cookbook-simple-volume-rendering with my file, but I always get this error:
> 
> 
> yt\units\yt_array.py:764: RuntimeWarning: divide by zero encountered in divide
>  return YTArray(super(YTArray, self).__rdiv__(lo))
> yt\data_objects\image_array.py:229: RuntimeWarning: invalid value encountered in multiply
>  np.multiply(self[:, :, :3], 1.0/cmax, out[:, :, :3])
> 
> 
> This is the complete log:
> 
> 
> yt : [INFO     ] 2015-05-29 20:51:30,302 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name
> yt : [INFO     ] 2015-05-29 20:51:30,302 integer runtime parameter forcedplotfilenumber overwrites a simulation scalar of the same name
> yt : [INFO     ] 2015-05-29 20:51:30,302 integer runtime parameter nbegin overwrites a simulation scalar of the same name
> yt : [INFO     ] 2015-05-29 20:51:30,302 integer runtime parameter particlefilenumber overwrites a simulation scalar of the same name
> yt : [INFO     ] 2015-05-29 20:51:30,302 integer runtime parameter plotfilenumber overwrites a simulation scalar of the same name
> yt : [INFO     ] 2015-05-29 20:51:30,331 Parameters: current_time              = 1.10472907814e+17
> yt : [INFO     ] 2015-05-29 20:51:30,331 Parameters: domain_dimensions         = [16 16 16]
> yt : [INFO     ] 2015-05-29 20:51:30,332 Parameters: domain_left_edge          = [ -2.20000000e+25  -2.20000000e+25  -2.20000000e+25]
> yt : [INFO     ] 2015-05-29 20:51:30,332 Parameters: domain_right_edge         = [  2.20000000e+25   2.20000000e+25   2.20000000e+25]
> yt : [INFO     ] 2015-05-29 20:51:30,332 Parameters: cosmological_simulation   = 0.0
> yt : [INFO     ] 2015-05-29 20:51:32,513 Loading field plugins.
> yt : [INFO     ] 2015-05-29 20:51:32,513 Loaded angular_momentum (8 new fields)
> yt : [INFO     ] 2015-05-29 20:51:32,515 Loaded astro (15 new fields)
> yt : [INFO     ] 2015-05-29 20:51:32,515 Loaded cosmology (22 new fields)
> yt : [WARNING  ] 2015-05-29 20:51:32,515 Field ('gas', 'number_density') already exists. To override use force_override=True.
> yt : [INFO     ] 2015-05-29 20:51:32,516 Loaded fluid (63 new fields)
> yt : [INFO     ] 2015-05-29 20:51:32,516 Loaded fluid_vector (95 new fields)
> yt : [INFO     ] 2015-05-29 20:51:32,516 Loaded geometric (111 new fields)
> yt : [INFO     ] 2015-05-29 20:51:32,517 Loaded local (111 new fields)
> yt : [INFO     ] 2015-05-29 20:51:32,517 Loaded magnetic_field (119 new fields)
> yt : [INFO     ] 2015-05-29 20:51:32,519 Loaded my_plugins (119 new fields)
> yt : [INFO     ] 2015-05-29 20:51:32,519 Loaded species (121 new fields)
> yt : [INFO     ] 2015-05-29 20:51:42,595 Warning: no_ghost is currently True (default). This may lead to artifacts at grid boundaries.
> Ray casting100% ||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:01
> C:\Anaconda\lib\site-packages\yt\units\yt_array.py:764: RuntimeWarning: divide by zero encountered in divide
>  return YTArray(super(YTArray, self).__rdiv__(lo))
> C:\Anaconda\lib\site-packages\yt\data_objects\image_array.py:229: RuntimeWarning: invalid value encountered in multiply
>  np.multiply(self[:, :, :3], 1.0/cmax, out[:, :, :3])
> 
> The image itself is created, but only black, also the rendering process is instantly finished.
> 
> I've tried it with the "Enzo_64/DD0043/data0043" file as used for the tutorial, this works with errors. Then I've tried using a given FLASH dataset, the "GalaxyClusterMerger" - same result as my dataset, also the error.
> 
> I'm using Win 8.1 64-bit Anaconda distribution and yt-project 3.1. Also tried the same thing on Ubuntu 14 with freshly installed yt-project, same error.
> 
> Is there a solution to create a volume render with FLASH files?
> 
> Thank you for your attention!
> 
> Kilian
> 
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