[yt-users] Cell Volume in regions

Nathan Goldbaum nathan12343 at gmail.com
Thu Jul 10 07:30:56 PDT 2014


Sorry for all the questions, but this is very puzzling.  Can you share the
exact script you're using?  If the dataset is small enough and it's ok to
share, it would also help to see the dataset as well.  We've used dropbox
or google drive to share these sorts of files in the past with a lot of
success.


On Thu, Jul 10, 2014 at 3:48 AM, Daniel <cunnama at gmail.com> wrote:

> Hi Desika,
>
> If I read the log right the latest change is:
>
> changeset:   12732:c9e843865b2a
> branch:      yt
> tag:         tip
> parent:      12499:1b93a1840f38
> user:        dcollins4096
> date:        Sun Jul 06 20:08:39 2014 -0400
>
> Thanks,
> Daniel
>
>
> On 10 July 2014 10:08, Desika Narayanan <dnarayan at haverford.edu> wrote:
>
>> Hi Daniel,
>>
>> Which changeset are you on?  (Matt can correct me on this) but I think
>> there was a time when the default was that over_refine_factor = 1.
>>  Though that wouldn't explain equal cell and particle numbers...
>>
>> -d
>>
>>
>> On Wed, Jul 9, 2014 at 3:29 PM, Daniel <cunnama at gmail.com> wrote:
>>
>>> I was comparing density and temperature to the cell_volume.
>>>
>>>
>>> On 9 July 2014 20:04, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>>>
>>>> Which fields were you comparing with?
>>>>
>>>>
>>>> On Wednesday, July 9, 2014, Daniel <cunnama at gmail.com> wrote:
>>>>
>>>>> Hi Matt,
>>>>>
>>>>> No, just loading a standard GadgetDataset:
>>>>>
>>>>> bbox = [[0.0, 1000000.0],
>>>>>         [0.0, 1000000.0],
>>>>>         [0.0, 1000000.0]]
>>>>>
>>>>> unit_base = {'UnitLength_in_cm'         : 3.08568e+21,
>>>>>              'UnitMass_in_g'            :   1.989e+43,
>>>>>              'UnitVelocity_in_cm_per_s' :      100000}
>>>>>
>>>>> pf = GadgetDataset("snapshot_050", unit_base = unit_base, bounding_box
>>>>> = bbox)
>>>>>
>>>>> Cheers,
>>>>> Daniel
>>>>>
>>>>>
>>>>> On 9 July 2014 17:58, Matthew Turk <matthewturk at gmail.com> wrote:
>>>>>
>>>>>> Hi Daniel,
>>>>>>
>>>>>> On Wed, Jul 9, 2014 at 10:57 AM, Daniel <cunnama at gmail.com> wrote:
>>>>>> > Hi Nathan,
>>>>>> >
>>>>>> > Thanks for getting back to me.
>>>>>> >
>>>>>> > That is odd, because then if my region includes all the particles I
>>>>>> have
>>>>>> > equal elements in cell_volume and all the other gas quantities?
>>>>>> >
>>>>>>
>>>>>> Yup, that is a bit odd.  How are you loading the data?  Are you
>>>>>> specifying either n_ref or over_refine_factor when doing so?
>>>>>>
>>>>>> -Matt
>>>>>>
>>>>>> > Kind Regards,
>>>>>> > Daniel
>>>>>> >
>>>>>> >
>>>>>> > On 9 July 2014 15:06, Nathan Goldbaum <nathan12343 at gmail.com>
>>>>>> wrote:
>>>>>> >>
>>>>>> >> Hi Daniel,
>>>>>> >>
>>>>>> >> The cell_volume field is an alias for ('gas, 'cell_volume'), which
>>>>>> for
>>>>>> >> Gadget data corresponds to the volume of octree cells. In general
>>>>>> there will
>>>>>> >> be fewer octree cells than particles.  I'm a little surprised the
>>>>>> numbers
>>>>>> >> are so close since the default option is to refine octree cells
>>>>>> when more
>>>>>> >> than 64 particles are in a cell, although the precise structure of
>>>>>> the
>>>>>> >> octree will depend on the particle distribution.
>>>>>> >>
>>>>>> >> Nathan
>>>>>> >>
>>>>>> >>
>>>>>> >> On Wednesday, July 9, 2014, Daniel <cunnama at gmail.com> wrote:
>>>>>> >>>
>>>>>> >>> Hi there,
>>>>>> >>>
>>>>>> >>> I am extracting a region from a Gadget dataset using the sphere
>>>>>> function
>>>>>> >>> and then attempting to access the "cell_volume" field.
>>>>>> >>>
>>>>>> >>> For some reason the number of elements in the cell volume field
>>>>>> is not
>>>>>> >>> equal to the number of particles in the region.
>>>>>> >>>
>>>>>> >>> For example I have 4341760 particles but only 4228930 cell volume
>>>>>> >>> elements.
>>>>>> >>>
>>>>>> >>> I have extracted a sphere which encompassed all the particles and
>>>>>> the
>>>>>> >>> number of cell volume elements is then equal.
>>>>>> >>>
>>>>>> >>> Any ideas or advice would be greatly appreciated.
>>>>>> >>>
>>>>>> >>> Kind Regards,
>>>>>> >>> Daniel
>>>>>> >>
>>>>>> >>
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>>>>>> >>
>>>>>> >
>>>>>> >
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