Rendering Volume of FLASH file
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-... 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
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@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-... 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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Suoqing JI