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@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@gmail.com> wrote:

On Thu, Aug 11, 2016 at 11:03 AM, Chang-Goo Kim <cgkim@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@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@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@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@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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