[yt-users] chemical species abundances discrepancy

Matthew Turk matthewturk at gmail.com
Fri Jan 31 05:26:18 PST 2014


On Fri, Jan 31, 2014 at 2:58 AM, poetaste at gmail.com <poetaste at gmail.com> wrote:
> Hi Britton and Matt,
> thanks very much for the clarification... the mathematics is clear but my
> question is the following:
>
> If I have a new species which is not defined in YT as _Fraction and I would
> like to plot the mass fraction, how can I avoid such problems with the
> average quantities and binning?
> Which is the right procedure starting from the mass density obtained from
> enzo (species_Density)?

Create a new derived field:

http://yt-project.org/docs/2.6/analyzing/creating_derived_fields.html

-Matt

>
> Thanks in advance
> Stefano
>
> Il giorno 27/gen/14, alle ore 18:34, Britton Smith ha scritto:
>
> The reason the answers are getting closer together when you add more bins is
> that you are decreasing the number of points in each bin, and as you do that
> the difference between
> mean(f * g) and mean(f) * mean(g) will get smaller, though it will not be
> identical until you have exactly one cell in each bin.
>
>
> On Mon, Jan 27, 2014 at 5:29 PM, Stefano Bovino <poetaste at gmail.com> wrote:
>>
>> Ah ok,
>> it seems that increasing a lot the number of bins the two approaches are
>> matching better... is there any reason for that?
>>
>> A second question: how it works for the electrons? In enzo the electrons
>> are usually initialized considering a factor of mp/me, YT takes into account
>> this rescaling?
>>
>> Thanks again
>> Stefano
>>
>>
>> On Mon, Jan 27, 2014 at 6:24 PM, Stefano Bovino <poetaste at gmail.com>
>> wrote:
>>>
>>> ah... I'm binning, it also depends on the number of bins I'm using, but
>>> the discrepancy (slight) is still there):
>>>
>>> prof3 = BinnedProfile1D(sph3, 64, "Radiuspc", 1.0e-6, 1.0e6)
>>>
>>> In my initial setup I'm using a box of 300 pc.
>>>
>>> Stefano
>>>
>>>
>>> On Mon, Jan 27, 2014 at 6:20 PM, Stefano Bovino <poetaste at gmail.com>
>>> wrote:
>>>>
>>>> Hi Matt,
>>>> thanks for the quick reply.
>>>> I'm using simple data from the enzo Collapse Test (27).
>>>> It seems is mainly related to the size of the sphere I'm taking... but I
>>>> don't know.
>>>>
>>>> Here following a piece of my script:
>>>>
>>>>  pf3=load("DD0003/DD0003")
>>>> c3= pf3.h.find_max("Density")[1]
>>>> sph3 = pf3.h.sphere(c3, (100, 'pc'))
>>>> prof3.add_fields("H2I_Density")
>>>> prof3.add_fields("H2I_Fraction")
>>>> prof3.add_fields("Radius")
>>>>
>>>> ...
>>>> ...
>>>>
>>>> d_ax2.loglog(prof3['Radius'], prof3['H2I_Density']/prof3['Density'],
>>>>             lw=1.5, linestyle='--', color='r')
>>>> d_ax2.loglog(prof3['Radius'], prof3['H2I_Fraction'],
>>>>             lw=1.5, linestyle=':', color='y')
>>>>
>>>> Thanks in advance
>>>> Stefano
>>>>
>>>>
>>>> On Mon, Jan 27, 2014 at 6:11 PM, Matthew Turk <matthewturk at gmail.com>
>>>> wrote:
>>>>>
>>>>> On Mon, Jan 27, 2014 at 12:14 PM, poetaste at gmail.com
>>>>> <poetaste at gmail.com> wrote:
>>>>> > Hi Guys,
>>>>> > I did a simple test with enzo and I tried to plot a radial profile of
>>>>> > the
>>>>> > chemical species fractions with YT.
>>>>> >
>>>>> > The problem is that if I use the YT function which intrinsically plot
>>>>> > the
>>>>> > fraction for a species, let's say H2I_Fraction (as usual), and
>>>>> > compare this
>>>>> > with a direct evaluation of the mass fraction:
>>>>> >
>>>>> > data['H2I_Density']/data['Density']
>>>>> >
>>>>> > I obtain some slightly different results, mostly at large radii.
>>>>> >
>>>>> > Anyone might explain this discrepancy!? This happens with all the
>>>>> > species.
>>>>>
>>>>> Without knowing what "data" here is, or how you generated it, it's
>>>>> tough to say.
>>>>>
>>>>> -Matt
>>>>>
>>>>> >
>>>>> > Thank you in advance
>>>>> > Stefano_______________________________________________
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>>
>>
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