[yt-users] add particle information to ds

Thu Aug 11 10:47:48 PDT 2016

Thanks, there's no hurry for this specific case.

I have another problem with magnetic field units. I set unit conversion
factors with 'unit_override' keyword. These are the units I'm using

>>> print ya.unit_base

{'length_unit': (1.0, 'pc'),
 'mass_unit': (2.38858753789e-24, 'g/cm**3*pc**3'),
 'time_unit': (1.0, 's*pc/km')}

This should set the magnetic field unit as follows:

>>>
mu=yt.YTQuantity(ya.unit_base['mass_unit'][0],ya.unit_base['mass_unit'][1])
>>>
lu=yt.YTQuantity(ya.unit_base['length_unit'][0],ya.unit_base['length_unit'][1])
>>>
tu=yt.YTQuantity(ya.unit_base['time_unit'][0],ya.unit_base['time_unit'][1])
>>> mag_unit=(np.sqrt(4*np.pi*mu/lu)/tu)
>>> print mag_unit.convert_to_units('gauss')

5.4786746797e-07 gauss

But, what I found in the unit_registry is a bit strange number.

>>> print ds.unit_registry['code_magnetic']

(3.5449077018110318,
 sqrt((mass))/(sqrt((length))*(time)),
 0.0,
 '\\rm{code\\ magnetic}')

It seems that "magnetic_unit" was set correctly in
yt/frontends/athena/data_structures.py:

        self.magnetic_unit = np.sqrt(4*np.pi * self.mass_unit /
                                     (self.time_unit**2 * self.length_unit))
        self.magnetic_unit.convert_to_units("gauss")

I don't know what's wrong here. Do you have any idea?

Thanks,
Chang-Goo

On Thu, Aug 11, 2016 at 12:12 PM, John Zuhone <jzuhone at gmail.com> wrote:

> We can add in a particle_file keyword argument like we do for FLASH data.
>
> I can help out with this, but I might not be able to get to it until early
> next week.
>
> On Aug 11, 2016, at 12:11 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>
>
> On Thu, Aug 11, 2016 at 11:03 AM, Chang-Goo Kim <cgkim at astro.princeton.edu
> > wrote:
>
>> Hi Nathan,
>>
>> Thanks for the reply. Adding particles to the athena frontend will not be
>> easy since there is no unified (and well settled) data dump for particles.
>> Star particles are not in the public release. Let me find other ways at
>> this point.
>>
>>
> Ah, in that case we should probably add a way for you to supply your own
> particle data. You won't get chunked particle IO but if that's sufficient
> it should probably be straightforward to load the data in as a keyword
> argument for the load() command.
>
> John might have some insight on what's best to do here, he's the
> maintainer of the athena frontend.
>
> -Nathan
>
>
>> Thanks,
>> Chang-Goo
>>
>>
>> On Thu, Aug 11, 2016 at 11:35 AM, Nathan Goldbaum <nathan12343 at gmail.com>
>>  wrote:
>>
>>> I think we'd need to add support for reading particle data to the athena
>>> frontend. I think the main reason this hasn't been done yet is lack of
>>> available test datasets. If you'd like to make one or more test datasets
>>> available to us (they will live on yt-project.org/data so we can use
>>> them for testing and debugging going forward), someone could try to add
>>> support for reading particle data to the Athena frontend.
>>>
>>> To answer your question, no, there isn't a way to add particle fields to
>>> an athena dataset without modifying the athena frontend.
>>>
>>> That said, you might be able to cheat and load in the particle fields
>>> using the stream frontend to reload your data as an in-memory dataset - in
>>> particular load_uniform_grid or load_amr_grids. Of course this is sort of a
>>> hack, ideally we'd just add particle support to the athena frontend.
>>>
>>> -Nathan
>>>
>>> -Nathan
>>>
>>> On Thu, Aug 11, 2016 at 10:32 AM, Chang-Goo Kim <
>>> cgkim at astro.princeton.edu> wrote:
>>>
>>>> Sorry for confusion.
>>>>
>>>> I have a separate vtk file for star particles. Just wonder whether I
>>>> can add this to original dataset as fields to handle them together.
>>>>
>>>> Thanks,
>>>> Chang-Goo
>>>>
>>>> On Wed, Aug 10, 2016 at 3:19 PM, John Zuhone <jzuhone at gmail.com> wrote:
>>>>
>>>>> Hi Chang-Goo,
>>>>>
>>>>> > When I load the dataset from Athena and I have star particle mass,
>>>>> position, velocity, age information separately,
>>>>>
>>>>> Sorry, I’m a bit confused as to what you mean by this, because as far
>>>>> as I know we don’t have particle support for Athena data yet. Do you
>>>>> actually see the particle data when you load the dataset? Also, is this the
>>>>> old Athena or Athena++?
>>>>>
>>>>> > how can I add particle information to yt dataset.
>>>>>
>>>>> I think by this you mean getting the particle fields into yt, correct?
>>>>> Just making sure.
>>>>>
>>>>> Is the data part of the Athena file itself or is it in a separate file?
>>>>>
>>>>> Best,
>>>>>
>>>>> John
>>>>>
>>>>> > On Aug 10, 2016, at 2:24 PM, Chang-Goo Kim <changgoo at princeton.edu>
>>>>> wrote:
>>>>> >
>>>>> > Hi all,
>>>>> >
>>>>> > I'm analysing data from Athena simulations with star particles. When
>>>>> I load the dataset from Athena and I have star particle mass, position,
>>>>> velocity, age information separately, how can I add particle information to
>>>>> yt dataset. I tried to look up the hep, but I cannot find any good
>>>>> reference for this issue.
>>>>> >
>>>>> > Thanks,
>>>>> > Chang-Goo
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