[yt-users] RAMSES units bug in yt-3.0

Tue May 13 05:01:33 PDT 2014

I had a chance to test out an older and a newer version of yt-3 on a small
dataset that has boxlen=10. This seems to confirm a boxlen**3 factor
somewhere, although there's a further difference in the max density.

more recent version (hg id -i gives f4838a2165c0):

after dd = ds.all_data():

In [11]: dd.quantities.extrema('density')

Out[11]: (2.00739832795e-28 g/cm**3, 4.54771338163e-24 g/cm**3)

older version (hg id -i gives 3e8b733c9ee9):

after dd = ds.h.all_data():

In [10]: dd.quantities.extrema('Density')

Out[10]: [(2.0073983279492632e-25, 4.0079147772594363e-21)]

On Fri, May 9, 2014 at 5:50 PM, Sam Geen <samgeen at astro.ox.ac.uk> wrote:

> Yep, that looks like it should work. I'll try to run it on some particle
> data when I get the time, but like I said I'm 99% sure the mass units
> should be identical for both grid hydro and particle data.
>
>
> On 09/05/14 17:46, Matthew Turk wrote:
>
>> Hi Sam,
>>
>> Okay, I've looked over a bit, and I think the correct change would be:
>>
>> mass_unit = rho_u * length_unit**3.
>>
>> That should include the correct length unit, and I think will reduce
>> "density" back to the "unit_d" that's in the parameter file.  If this
>> looks okay to you, I will push it, but I really do want to make sure
>> the particle masses are correct.  Can Nick or Romain provide a bit of
>> guidance here?
>>
>> -Matt
>>
>> On Fri, May 9, 2014 at 11:25 AM, Sam Geen <samgeen at astro.ox.ac.uk> wrote:
>>
>>> OK, interesting. In theory RAMSES should have identical units for both
>>> particles and gas. I can hunt down a run with particles to test if you
>>> like.
>>>
>>> Thanks!
>>> Sam
>>>
>>>
>>> On 09/05/14 17:22, Matthew Turk wrote:
>>>
>>>> Hi Sam,
>>>>
>>>> On reflection, I think this might be related to getting the *particle*
>>>> masses correct.  I will take a look at it as soon as I can.
>>>>
>>>> -Matt
>>>>
>>>> On Fri, May 9, 2014 at 11:00 AM, Sam Geen <samgeen at astro.ox.ac.uk>
>>>> wrote:
>>>>
>>>>> Hmm, that looks like it should be "mass_unit = rho_u * length_unit**3"
>>>>> in
>>>>> line 492. You're right that it mentions the boxlength issue, though.
>>>>>
>>>>>
>>>>> On 09/05/14 16:50, Matthew Turk wrote:
>>>>>
>>>>>> Hi Sam,
>>>>>>
>>>>>> Okay, sounds good.  Looking at how code unit attributes are set up:
>>>>>>
>>>>>>
>>>>>>
>>>>>> https://bitbucket.org/yt_analysis/yt/src/
>>>>>> a14a150c7c81850df81346162bdaff271e77eb50/yt/frontends/
>>>>>> ramses/data_structures.py?at=yt-3.0#cl-482
>>>>>>
>>>>>> suggests to me that length_unit takes into account boxlen, and
>>>>>> mass_unit does not.  The comments have some indication why this might
>>>>>> be.
>>>>>>
>>>>>> -Matt
>>>>>>
>>>>>> On Fri, May 9, 2014 at 10:46 AM, Sam Geen <samgeen at astro.ox.ac.uk>
>>>>>> wrote:
>>>>>>
>>>>>>> Yep; both this and dd["density"] give cgs values that are too small
>>>>>>> by
>>>>>>> roughly a factor of boxlen**3.
>>>>>>>
>>>>>>> One other thing I need to try is to make sure I'm using the very
>>>>>>> latest
>>>>>>> version of YT; I've been playing around with the Ramses frontend so
>>>>>>> it's
>>>>>>> possible my version is somehow out of sync. Will let you know if this
>>>>>>> fixes
>>>>>>> things.
>>>>>>>
>>>>>>>
>>>>>>> On 09/05/14 16:42, Matthew Turk wrote:
>>>>>>>
>>>>>>>> Hi Sam,
>>>>>>>>
>>>>>>>> Can you verify the units are in fact incorrect in *cgs*?  Something
>>>>>>>> like this would work:
>>>>>>>>
>>>>>>>> ds = load(...)
>>>>>>>> dd = ds.all_data()
>>>>>>>> print dd.quantities.total_quantitiy("cell_mass").in_cgs()
>>>>>>>>
>>>>>>>> Your second message makes me wonder if there's just a slipup in how
>>>>>>>> the units are returned.
>>>>>>>>
>>>>>>>> -Matt
>>>>>>>>
>>>>>>>> On Fri, May 9, 2014 at 10:37 AM, Sam Geen <samgeen at astro.ox.ac.uk>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Sorry for the spam; a second bug I've seen is that the density and
>>>>>>>>> pressure
>>>>>>>>> unit labels on figures appears to be broken; it seems to print a
>>>>>>>>> latex-mangled code names for the units rather than the cgs name of
>>>>>>>>> the
>>>>>>>>> units; see attached example. Temperature is fine.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 09/05/14 16:28, Sam Geen wrote:
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> Just to say that in the latest version of yt-3.0 (i.e. since
>>>>>>>>>> various
>>>>>>>>>> fields were renamed or re-implemented), I've found a bug in the
>>>>>>>>>> implementation of "cell_mass", which is giving results that are
>>>>>>>>>> too
>>>>>>>>>> low
>>>>>>>>>> in
>>>>>>>>>> my runs; I believe the issue is that it's missing a factor of
>>>>>>>>>> pf["boxlen"]**3 (which is of course only a problem if boxlen is
>>>>>>>>>> not
>>>>>>>>>> 1).
>>>>>>>>>> The
>>>>>>>>>> previous "CellMass_Msun" worked fine. If I get time I might take a
>>>>>>>>>> look
>>>>>>>>>> and
>>>>>>>>>> issue a pull request, but otherwise I'm just flagging this in case
>>>>>>>>>> someone
>>>>>>>>>> else runs into problems; you can just manually multiply the result
>>>>>>>>>> by
>>>>>>>>>> pf["boxlen"]**3 until it's fixed.
>>>>>>>>>>
>>>>>>>>>> Cheers,
>>>>>>>>>>
>>>>>>>>>> Sam
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>>>>>>>>>
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