[yt-users] yt.lagrangian_volume

Wed Oct 29 06:49:11 PDT 2014

Yes, that's right, and the halo should be found at the new normalized
position of 0.5, 0.5, 0.5.  Good luck!

Cameron

On Tue, Oct 28, 2014 at 7:50 PM, Chen Jingjing <chenjj235 at gmail.com> wrote:

> Thanks! I think I got it.
> But just to make sure that I really understand it: so if I am tracing the
> box that contains all the particles which forms a halo at later stage, I
> will be using the bounding box whose values are the normalized position of
> the bottom left and top right corner of the box. Right?
>
> Jingjing
>
> 2014-10-28 16:17 GMT-04:00 Cameron Hummels <chummels at gmail.com>:
>
> It looks like there is substantial drift in your halos from the start
>> output to the final output.  As I mentioned previously, the first bounding
>> box is in the coordinate system of the earliest output.  When it goes above
>> 1, it's just referring to a periodic boundary.  The center of mass is of
>> the final halo in the later output file, and it doesn't have to be in the
>> bounding box if there is substantial drift of the halo from the early
>> output to the final output, as it appears there is in these simulations.
>> Are you choosing dwarf galaxies, which tend to be more susceptible to drift
>> in cosmological runs like this?
>>
>> The final output is the same as the first bounding box, but it has been
>> shifted over in space, so that the COM of the 2nd step sits at 0.5, 0.5,
>> 0.5.  This makes a lot more sense if you choose a halo which has no drift,
>> so its center of mass remains inside of the bounding box of the earliest
>> output.
>>
>> I'd suggest picking a galaxy which doesn't have so much drift for
>> re-simulation.  Let me know if you have any other questions!
>>
>> Cameron
>>
>>
>> On Tue, Oct 28, 2014 at 12:58 PM, Cameron Hummels <chummels at gmail.com>
>> wrote:
>>
>>> Oops.  I just saw that you did include the outputs.  Let me look into
>>> this and get back to you in a moment.
>>>
>>> Cameron
>>>
>>> On Tue, Oct 28, 2014 at 12:56 PM, Cameron Hummels <chummels at gmail.com>
>>> wrote:
>>>
>>>> Hi Jingjing,
>>>>
>>>> I'm sorry that you're running into some problems with
>>>> yt.lagrangian_region. Let me see if I can help you.
>>>>
>>>> The output of the code should return a box in code units containing all
>>>> of the DM particles in the selected halo.  I've only tested this with enzo
>>>> outputs (and I believe that is what you're using it on too), so those code
>>>> units will go from 0 to 1 in x, y, z.  In addition to this output, the code
>>>> also will recenter these coordinates so that the final halo coordinates
>>>> will sit at 0.5, 0.5, 0.5 at the center of the box.  It provides the
>>>> original box shifted over in coordinates to accomodate this recentering.
>>>> Lastly, you are correct that some of the coordinates will go above 1 in
>>>> cases when the particles shift over the periodic boundary condition.
>>>>
>>>> Do your results make more sense given this information?  If you're
>>>> still confused, can you send us the text of your outputs, so that we can
>>>> try to figure them out?
>>>>
>>>> I'm actually working on a newer version of this which will work with yt
>>>> 3.0 as part of a larger effort to make efficient zoom simulations, but I've
>>>> not yet finished working on it.  I'll make sure to announce it here when
>>>> this is complete and ready.
>>>>
>>>> Cameron
>>>>
>>>>
>>>> On Tue, Oct 28, 2014 at 12:00 PM, Chen Jingjing <chenjj235 at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>> I am using the code yt.lagrangian_volume to trace the box that
>>>>> contains the dark matter particles at an early stage(higher redshift). But
>>>>> I was quite confused about the output. I am attaching the output file
>>>>> below.
>>>>> (1) I don't know what the values for the box in the new frame mean,
>>>>> i.e. what is the unit of these values? It seems to be the normalized scale
>>>>> because the values are about 1. But it does not seem to be normalized too
>>>>> because there are some values that are larger than 1. Is that due to the
>>>>> periodicity of the box?
>>>>> (2) The bounding box and box in the new frame seems to have the same
>>>>> size. The difference between the two box is just translation. But I was
>>>>> expecting that the box should be expanding/collapsing.
>>>>> (3) The COM (center of mass) in the output is within neither of the
>>>>> box.
>>>>>
>>>>> Does anyone know how to explain the box values in the output file?
>>>>>
>>>>> Thanks,
>>>>> Jingjing
>>>>>
>>>>> --
>>>>>
>>>>> Jingjing Chen [ chenjj235 at gmail.com ]
>>>>> Department of Astronomy
>>>>> Columbia University
>>>>> 550 West 120th Street
>>>>> New York, New York 10027
>>>>> Cell Phone: +1(347)5746709
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> yt-users mailing list
>>>>> yt-users at lists.spacepope.org
>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Cameron Hummels
>>>> Postdoctoral Researcher
>>>> Steward Observatory
>>>> University of Arizona
>>>> http://chummels.org
>>>>
>>>
>>>
>>>
>>> --
>>> Cameron Hummels
>>> Postdoctoral Researcher
>>> Steward Observatory
>>> University of Arizona
>>> http://chummels.org
>>>
>>
>>
>>
>> --
>> Cameron Hummels
>> Postdoctoral Researcher
>> Steward Observatory
>> University of Arizona
>> http://chummels.org
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
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>>
>>
>
>
> --
>
> Jingjing Chen [ chenjj235 at gmail.com ]
> Department of Astronomy
> Columbia University
> 550 West 120th Street
> New York, New York 10027
> Cell Phone: +1(347)5746709
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>

-- 
Cameron Hummels
Postdoctoral Researcher
Steward Observatory
University of Arizona
http://chummels.org
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