[yt-users] yt.lagrangian_volume

Cameron Hummels chummels at gmail.com
Wed Oct 29 14:52:29 PDT 2014


The frame you choose doesn't really matter.  We included the
renormalization to center on where the galaxy would be at the later time
just as a convenience, but as you noticed, it just shifts things over, and
it doesn't change anything.

Good luck with your new refinement simulations.

Cameron

On Wed, Oct 29, 2014 at 11:21 AM, Chen Jingjing <chenjj235 at gmail.com> wrote:

> Hi Cameron,
> It seems that box containing the particles is too big for our afterwards
> simulation. The box contains ~500x mass of the halo mass, which means that
> we will be doing refined simulation on a lot of particles that we don't
> concern if we use that box. So we think that instead of finding the box, we
> will find the distribution of all the particles that forms the halo.
>
> What I am not sure about is, should I use the original frame or the
> periodic frame for each particle's position? Your comment in the code said
> that "it depends on which one gives a smaller extent in their frame. "
> However now that I am not considering a box, which means there is no
> extent, what is the criteria for choosing the frame?
>
> Thanks,
> Jingjing
>
>
> 2014-10-29 9:49 GMT-04:00 Cameron Hummels <chummels at gmail.com>:
>
> 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
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>>
>>>
>>>
>>> --
>>>
>>> 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
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>
>
> --
>
> 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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