[yt-users] chemical species abundances discrepancy

poetaste at gmail.com poetaste at gmail.com
Fri Jan 31 07:26:09 PST 2014 

thank you both for the help!
Make a derived fields seems to me the right direction!

Cheers,
Stefano

Il giorno 31/gen/14, alle ore 15:54, Britton Smith ha scritto:

> I agree with Matt. You can make a derived field that is the mass of  
> the species field and simply make profiles of the total mass in that  
> field and the total gas mass.  You can also make a derived field  
> that is the ratio of the density of that field to the total gas  
> density and then profile that with some weight field.  That will  
> give you another measurement that is different, but no less valid.   
> The important thing is to understand statistically what is being  
> calculated and make sure that you are comparing apples to apples.
>
>
> On Fri, Jan 31, 2014 at 8:26 AM, Matthew Turk  
> <matthewturk at gmail.com> wrote:
> 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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> >>>>> > yt-users at lists.spacepope.org
> >>>>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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> >>>>
> >>>>
> >>>
> >>
> >>
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