Hi John,<br><br>So, what I mean by "expected" variables are basically all variables BUT specific_scalar[0]. When I read in the vtk file, you can see that the bottom line says <br><br><pre>yt : [INFO ] 2012-12-13 23:27:13,214 Adding unknown field specific_scalar[0] to list of fields<br>
<br></pre>Yes, I can do any of the "quantities" commands, for example:<br><br>alld = pf.h.all_data()<br>tracerp25 = alld.cut_region(["grid['specific_scalar[0]'] > 0.25", "grid['z'] > 0.01"])<br>
<pre><span style="font-family:arial,helvetica,sans-serif">radmean = tracerp25.quantities["WeightedAverageQuantity"]("Radius","Ones")<br><br></span></pre>Slicing also works:<br><br>p = SlicePlot(pf,"x","specific_scalar[0]")<br>
<br>Now I am starting to worry that it is because output is so big--each vtk file is 72 MB, so a full output is almost 25 GB. When I just use two outputs (moving them so yt only sees id0 and id1 folders) the phase plot works. But, after running the add_phase_object command on the whole data set for more than 1.5 hours I still have no result and my computer keeps freezing--although top shows that only 42% of memory is being used. <br>
<br>Is it possible that my output is just too big?<br><br>Stephanie<br><br><br><div class="gmail_quote">On Tue, Dec 18, 2012 at 11:00 AM, John Zuhone <span dir="ltr"><<a href="mailto:jzuhone@gmail.com" target="_blank">jzuhone@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Stephanie,<div><br></div><div>Ok, thanks for checking that. </div><div><br></div><div>I guess I'm not sure what you mean by the "expected" set of variables. Do you mean the ones that yt defines, or the ones that are in the field list? It looks like "velocity_z" works for one call and doesn't for another. </div>
<div><br></div><div>Are you able to do anything else with "specific_scalar[0]"? Like make a slice, or a projection of some sort? Or maybe take the weighted average of it in a sphere. I'd be interested in seeing if the problem was restricted to phase plotting. </div>
<div><br></div><div>How big is the dataset, by the way? Is there something that fails in the same way that the both of us can test on? </div><div><br></div><div>Best,</div><div><br></div><div>John<div><div><br>
<br><div class="gmail_quote">
On Tue, Dec 18, 2012 at 10:53 AM, Stephanie Tonnesen <span dir="ltr"><<a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>Hi,<br><br>Yup. Just to be sure I updated again and reattempted to make the phase_object and python was Killed again.<br><br>Thanks!<span><font color="#888888"><br><br>Stephanie</font></span><div>
<div><br><br><br><div class="gmail_quote">On Tue, Dec 18, 2012 at 12:35 AM, John ZuHone <span dir="ltr"><<a href="mailto:jzuhone@gmail.com" target="_blank">jzuhone@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Stephanie,<div><br></div><div>Just want to make sure that you're using the latest version of the yt development tree--it contains some important Athena fixes that were put in a few weeks back.</div>
<div><br></div><div>If so, then we'll work from there to figure out what's gone wrong. </div><div><br></div><div>Best,</div><div><br></div><div>John</div><div><br></div><div><div><div><div><div>On Dec 17, 2012, at 5:44 PM, Stephanie Tonnesen <<a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a>> wrote:</div>
<br></div></div><blockquote type="cite"><div><div>Hi yt-users,<br><br>I am trying to make phase_objects of Athena data. I am able to make phase_objects if I use the "expected" set of variables (will show below), but kill my kernel or am kicked out of python if I try and use an "unknown field" read in from a set of vtk files. <br>
<br><br><br>from yt.mods import *<br><br>pf = load("id0/rps.0080.vtk")<br><br><pre>yt : [INFO ] 2012-12-13 23:27:08,678 Temporarily setting domain_right_edge = -domain_left_edge. This will be corrected automatically if it is not the case.
yt : [INFO ] 2012-12-13 23:27:08,974 Parameters: current_time = 40.00096
yt : [INFO ] 2012-12-13 23:27:08,974 Parameters: domain_dimensions = [1048 1048 655]
yt : [INFO ] 2012-12-13 23:27:08,975 Parameters: domain_left_edge = [-3.2 -3.2 -2. ]
yt : [INFO ] 2012-12-13 23:27:08,976 Parameters: domain_right_edge = [ 3.2 3.2 2. ]
yt : [INFO ] 2012-12-13 23:27:08,977 Parameters: cosmological_simulation = 0.0
yt : [INFO ] 2012-12-13 23:27:13,214 Adding unknown field specific_scalar[0] to list of fields<br><br></pre>pf.h.field_list<br><br><pre>['density',
'pressure',
'velocity_z',
'velocity_x',
'velocity_y',
'specific_scalar[0]']<br></pre>alld = pf.h.all_data()<br>tracerp25 = alld.cut_region(["grid['specific_scalar[0]'] > 0.25", "grid['z'] > 0.01"])<br><br>##These commands works:<br>
<pre><span style="font-family:arial,helvetica,sans-serif">radmean = tracerp25.quantities["WeightedAverageQuantity"]("Radius","Ones")
pc = PlotCollectionInteractive(pf)<br><br>pc.add_phase_object(alld,["z","velocity_z","CellMass"],weight=None)<br><br>#The calls below fail. There is no error message. If I am in iPython,
#the kernel dies. If I am running on a computer, it freezes and
#eventually I just get the message
#Killed
pc.add_phase_object(alld,["z","specific_scalar[0]","CellMass"],weight=None)
pc.add_phase_object(tracerp25,["z","velocity_z","CellMass"],weight=None)
#If I read in a single vtk file ("id122/rps-id122.0080.vtk") the above
#commands work</span></pre>Any help would be much appreciated! Thanks,<br><br>Stephanie<br></div></div>
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<br></blockquote></div><br><br clear="all"><div><br></div></div></div><span><font color="#888888">-- <br>John ZuHone<br><br>Postdoctoral Researcher<br>NASA/Goddard Space Flight Center<div><br><a href="mailto:jzuhone@gmail.com" target="_blank">jzuhone@gmail.com</a><br>
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