<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Kilian,<div class=""><br class=""></div><div class="">Are you using exactly the same script from the cookbook? I noticed that the domain of your dataset is quite large:</div><div class=""><br class=""></div><div class=""><blockquote type="cite" class="">yt : [INFO ] 2015-05-29 20:51:30,332 Parameters: domain_left_edge = [ -2.20000000e+25 -2.20000000e+25 -2.20000000e+25]<br class="">yt : [INFO ] 2015-05-29 20:51:30,332 Parameters: domain_right_edge = [ 2.20000000e+25 2.20000000e+25 2.20000000e+25]<br class=""></blockquote><br class=""></div><div class="">So I suggest to change the width “w" to be larger or comparable to your domain size, say, 5.e25:</div><div class=""><br class=""></div><div class=""><div class=""># Set the width of the image.</div><div class=""># Decreasing or increasing this value</div><div class=""># results in a zoom in or out.</div><div class="">W = 1.0</div></div><div class=""><br class=""><div apple-content-edited="true" class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Best wishes,</div><div class="">--</div><div class="">Suoqing JI</div><div class="">Ph.D Student</div><div class="">Department of Physics</div><div class="">University of California, Santa Barbara</div><div class=""><a href="http://web.physics.ucsb.edu/~suoqing" class="">http://web.physics.ucsb.edu/~suoqing</a></div></div></div></div></div>
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<br class=""><div><blockquote type="cite" class=""><div class="">On May 29, 2015, at 12:19 PM, Kilian Gärtner <<a href="mailto:kilian.gaertner@st.ovgu.de" class="">kilian.gaertner@st.ovgu.de</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">Hi,<br class=""><br class="">I want to render a Volume Plot based on data from a FLASH file, which uses HDF5 file format. I tried the tutorial at <a href="http://yt-project.org/doc/cookbook/simple_plots.html#cookbook-simple-volume-rendering" class="">http://yt-project.org/doc/cookbook/simple_plots.html#cookbook-simple-volume-rendering</a> with my file, but I always get this error:<br class=""><br class=""><br class="">yt\units\yt_array.py:764: RuntimeWarning: divide by zero encountered in divide<br class=""> return YTArray(super(YTArray, self).__rdiv__(lo))<br class="">yt\data_objects\image_array.py:229: RuntimeWarning: invalid value encountered in multiply<br class=""> np.multiply(self[:, :, :3], 1.0/cmax, out[:, :, :3])<br class=""><br class=""><br class="">This is the complete log:<br class=""><br class=""><br class="">yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name<br class="">yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter forcedplotfilenumber overwrites a simulation scalar of the same name<br class="">yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter nbegin overwrites a simulation scalar of the same name<br class="">yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter particlefilenumber overwrites a simulation scalar of the same name<br class="">yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter plotfilenumber overwrites a simulation scalar of the same name<br class="">yt : [INFO ] 2015-05-29 20:51:30,331 Parameters: current_time = 1.10472907814e+17<br class="">yt : [INFO ] 2015-05-29 20:51:30,331 Parameters: domain_dimensions = [16 16 16]<br class="">yt : [INFO ] 2015-05-29 20:51:30,332 Parameters: domain_left_edge = [ -2.20000000e+25 -2.20000000e+25 -2.20000000e+25]<br class="">yt : [INFO ] 2015-05-29 20:51:30,332 Parameters: domain_right_edge = [ 2.20000000e+25 2.20000000e+25 2.20000000e+25]<br class="">yt : [INFO ] 2015-05-29 20:51:30,332 Parameters: cosmological_simulation = 0.0<br class="">yt : [INFO ] 2015-05-29 20:51:32,513 Loading field plugins.<br class="">yt : [INFO ] 2015-05-29 20:51:32,513 Loaded angular_momentum (8 new fields)<br class="">yt : [INFO ] 2015-05-29 20:51:32,515 Loaded astro (15 new fields)<br class="">yt : [INFO ] 2015-05-29 20:51:32,515 Loaded cosmology (22 new fields)<br class="">yt : [WARNING ] 2015-05-29 20:51:32,515 Field ('gas', 'number_density') already exists. To override use force_override=True.<br class="">yt : [INFO ] 2015-05-29 20:51:32,516 Loaded fluid (63 new fields)<br class="">yt : [INFO ] 2015-05-29 20:51:32,516 Loaded fluid_vector (95 new fields)<br class="">yt : [INFO ] 2015-05-29 20:51:32,516 Loaded geometric (111 new fields)<br class="">yt : [INFO ] 2015-05-29 20:51:32,517 Loaded local (111 new fields)<br class="">yt : [INFO ] 2015-05-29 20:51:32,517 Loaded magnetic_field (119 new fields)<br class="">yt : [INFO ] 2015-05-29 20:51:32,519 Loaded my_plugins (119 new fields)<br class="">yt : [INFO ] 2015-05-29 20:51:32,519 Loaded species (121 new fields)<br class="">yt : [INFO ] 2015-05-29 20:51:42,595 Warning: no_ghost is currently True (default). This may lead to artifacts at grid boundaries.<br class="">Ray casting100% ||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:01<br class="">C:\Anaconda\lib\site-packages\yt\units\yt_array.py:764: RuntimeWarning: divide by zero encountered in divide<br class=""> return YTArray(super(YTArray, self).__rdiv__(lo))<br class="">C:\Anaconda\lib\site-packages\yt\data_objects\image_array.py:229: RuntimeWarning: invalid value encountered in multiply<br class=""> np.multiply(self[:, :, :3], 1.0/cmax, out[:, :, :3])<br class=""><br class="">The image itself is created, but only black, also the rendering process is instantly finished.<br class=""><br class="">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.<br class=""><br class="">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.<br class=""><br class="">Is there a solution to create a volume render with FLASH files?<br class=""><br class="">Thank you for your attention!<br class=""><br class="">Kilian<br class=""><br class="">_______________________________________________<br class="">yt-users mailing list<br class=""><a href="mailto:yt-users@lists.spacepope.org" class="">yt-users@lists.spacepope.org</a><br class="">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org<br class=""></div></blockquote></div><br class=""></div></body></html>