On May 29, 2015, at 12:19 PM, Kilian Gärtner <kilian.gaertner@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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