<p dir="ltr">Thank you very much, I really appreciate the help!<br>
-Jared</p>
<div class="gmail_quote">On Aug 11, 2014 9:44 AM, "Matthew Turk" <<a href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Jared,<br>
<br>
I've found the bug and issued a fix, here:<br>
<br>
<a href="https://bitbucket.org/yt_analysis/yt/pull-request/1140/adding-check-for-no-fields-ptypes-in/diff" target="_blank">https://bitbucket.org/yt_analysis/yt/pull-request/1140/adding-check-for-no-fields-ptypes-in/diff</a><br>
<br>
Should go in shortly. (I put up a projection just for fun.)<br>
<br>
-Matt<br>
<br>
On Fri, Aug 8, 2014 at 5:21 PM, Jared Coughlin<br>
<<a href="mailto:Jared.W.Coughlin.29@nd.edu">Jared.W.Coughlin.29@nd.edu</a>> wrote:<br>
> No problem, thank you very much for all your help, I really appreciate it!<br>
> -Jared<br>
><br>
> On Aug 8, 2014 5:48 PM, "Nathan Goldbaum" <<a href="mailto:nathan12343@gmail.com">nathan12343@gmail.com</a>> wrote:<br>
>><br>
>> Ok, I can trigger the error you're seeing locally. I've passed this on to<br>
>> Matt who can take a closer look at what's happening and hopefully fix the<br>
>> issue you're running into.<br>
>><br>
>> Sorry for the difficulties, hopefully we'll have this cleared up soon.<br>
>> Thanks also for reporting this and working with us.<br>
>><br>
>><br>
>> On Fri, Aug 8, 2014 at 12:55 PM, Jared Coughlin<br>
>> <<a href="mailto:Jared.W.Coughlin.29@nd.edu">Jared.W.Coughlin.29@nd.edu</a>> wrote:<br>
>>><br>
>>> Hi,<br>
>>> I tried changing the units, and that gave the same error. I also tried<br>
>>> changing the center to 'c', and same thing. I've posted the contents of<br>
>>> ds.field_list and ds.derived_field_list here:<br>
>>> <a href="http://paste.yt-project.org/show/5003/" target="_blank">http://paste.yt-project.org/show/5003/</a><br>
>>><br>
>>> The plot of ('deposit'', 'Gas_smoothed_Density') also didn't work. The<br>
>>> traceback is here: <a href="http://paste.yt-project.org/show/5004/" target="_blank">http://paste.yt-project.org/show/5004/</a><br>
>>><br>
>>> The plot of ('deposit', 'all_cic') worked, however. At least, it ran and<br>
>>> produced an image without throwing any errors. I can upload the image to<br>
>>> google drive, if you'd like?<br>
>>><br>
>>> As for the snapshot, it's not very big, only 2.2M. I can put that on<br>
>>> google drive as well. Also, it's little endian. I can upload the parameter<br>
>>> file and ic file, as well, if you'd like.<br>
>>> -Jared<br>
>>><br>
>>><br>
>>><br>
>>><br>
>>> On Fri, Aug 8, 2014 at 1:51 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com">nathan12343@gmail.com</a>><br>
>>> wrote:<br>
>>>><br>
>>>> Hi Jared,<br>
>>>><br>
>>>> Looking at the traceback, it seems the issue is in calculating the<br>
>>>> maximum gas density in the simulation. I'm not sure why this is failing,<br>
>>>> but to see if we can create a plot at all, can you try supplying 'c' as the<br>
>>>> plot center instead of 'm'?<br>
>>>><br>
>>>> Can you also paste the contents of 'ds.field_list' and<br>
>>>> 'ds.derived_field_list'?<br>
>>>><br>
>>>> Additionally, can you create a SlicePlot of one of the following fields:<br>
>>>><br>
>>>> ('deposit', 'Gas_smoothed_Density')<br>
>>>> ('deposit', 'all_cic')<br>
>>>><br>
>>>> The first is another name for the SPH smoothed gas density - I'm<br>
>>>> checking here whether the ('gas', 'density') alias is misbehaving. The<br>
>>>> second is the cloud-in-cell deposited density for all particles in the<br>
>>>> simulation - I want to make sure that deposition isn't completely broken for<br>
>>>> your dataset.<br>
>>>><br>
>>>> Lastly, if the dataset isn't enormous and it is ok to share it, it would<br>
>>>> be helpful if you could share the actual dataset so one of us can reproduce<br>
>>>> your problem locally. We've had a lot of success using dropbox and google<br>
>>>> drive for this purpose in the past.<br>
>>>><br>
>>>> Hopefully we'll be able to get to the bottom of this,<br>
>>>><br>
>>>> Nathan<br>
>>>><br>
>>>><br>
>>>><br>
>>>> On Fri, Aug 8, 2014 at 9:39 AM, Jared Coughlin<br>
>>>> <<a href="mailto:Jared.W.Coughlin.29@nd.edu">Jared.W.Coughlin.29@nd.edu</a>> wrote:<br>
>>>>><br>
>>>>> Hi Nathan,<br>
>>>>> Thank you for responding! I tried what you suggested, but still no<br>
>>>>> luck. I'm still getting the index out of bounds error. I've copied the<br>
>>>>> traceback to the paste bin at: <a href="http://paste.yt-project.org/show/5001/" target="_blank">http://paste.yt-project.org/show/5001/</a><br>
>>>>> I've included how I loaded the snapshot as well as the call to<br>
>>>>> yt.SlicePlot, in case that helps. Thank you very much for all the help!<br>
>>>>> -Jared<br>
>>>>><br>
>>>>><br>
>>>>> On Thu, Aug 7, 2014 at 5:12 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com">nathan12343@gmail.com</a>><br>
>>>>> wrote:<br>
>>>>>><br>
>>>>>> Hi Jared,<br>
>>>>>><br>
>>>>>> Try instead:<br>
>>>>>><br>
>>>>>> yt.SlicePlot(ds, 'z', ('gas', 'density'), width=(10000., 'kpc'),<br>
>>>>>> center ='m')<br>
>>>>>><br>
>>>>>> (note the lower-case).<br>
>>>>>><br>
>>>>>> ('Gas', 'Density') is a particle field, i.e. the Density values<br>
>>>>>> associated with each of the Gas particles in your simulation. ('gas',<br>
>>>>>> 'density') is a mesh field - for SPH it is the smoothed gas density, taken<br>
>>>>>> from the original Gas particles. Particle fields are unstructured, the<br>
>>>>>> field is only defined at the positions where particles exist. Mesh fields<br>
>>>>>> are defined over the whole simulation domain.<br>
>>>>>><br>
>>>>>> Unfortunately there's some name collision here for gadget binary files<br>
>>>>>> so I can see how this is confusing. At the very least we should catch that<br>
>>>>>> you're trying to create a SlicePlot of a particle field and crash with a<br>
>>>>>> nicer, more understandable error.<br>
>>>>>><br>
>>>>>> More detail on the difference between particle and mesh fields as well<br>
>>>>>> as fields in yt in general here:<br>
>>>>>> <a href="http://yt-project.org/docs/3.0/analyzing/fields.html" target="_blank">http://yt-project.org/docs/3.0/analyzing/fields.html</a><br>
>>>>>><br>
>>>>>> Hope that helps,<br>
>>>>>><br>
>>>>>> -Nathan<br>
>>>>>><br>
>>>>>><br>
>>>>>> On Thu, Aug 7, 2014 at 2:08 PM, Jared Coughlin<br>
>>>>>> <<a href="mailto:Jared.W.Coughlin.29@nd.edu">Jared.W.Coughlin.29@nd.edu</a>> wrote:<br>
>>>>>>><br>
>>>>>>> Hi Nathan, I pasted the traceback here:<br>
>>>>>>> <a href="http://paste.yt-project.org/show/4998/" target="_blank">http://paste.yt-project.org/show/4998/</a><br>
>>>>>>> -Jared<br>
>>>>>>><br>
>>>>>>><br>
>>>>>>> On Thu, Aug 7, 2014 at 4:16 PM, Jared Coughlin<br>
>>>>>>> <<a href="mailto:Jared.W.Coughlin.29@nd.edu">Jared.W.Coughlin.29@nd.edu</a>> wrote:<br>
>>>>>>>><br>
>>>>>>>> Hello! I have a vanilla gadget snapshot (one from the lcdm sample<br>
>>>>>>>> run that the code comes with) that I was able to plot by following the<br>
>>>>>>>> instructions given here:<br>
>>>>>>>><br>
>>>>>>>> <a href="http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook" target="_blank">http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook</a><br>
>>>>>>>><br>
>>>>>>>> I then moved on to the 'Making Smoothed Images' section of that page<br>
>>>>>>>> and tried the SlicePlot command. However, I get the following error:<br>
>>>>>>>> IndexError: index 32767 is out of bounds for axis 0 with size 32767<br>
>>>>>>>><br>
>>>>>>>> Basically, I'm not really sure what that means. It seems like it's<br>
>>>>>>>> overstepping the bounds of an array, as, for a zero-indexed array of size<br>
>>>>>>>> 32767, index 32767 would be out of bounds by one. I just wanted to see if<br>
>>>>>>>> anyone else has had this problem, and if so, how they fixed it? Thank you<br>
>>>>>>>> very much!<br>
>>>>>>>> -Jared<br>
>>>>>>><br>
>>>>>>><br>
>>>>>>><br>
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>>>>>>><br>
>>>>>><br>
>>>>>><br>
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