[yt-users] different hydrogen densities from different versions of yt

Britton Smith brittonsmith at gmail.com
Fri Mar 3 14:06:26 PST 2017

Hi Nathan,

This is not a bug.  I will dig up the reference when I can, but at some
point it was decided that X_density should alias to X_p0_density, for
whatever X is.  Actually, I believe that this may go all the way back to
when this naming convention was decided upon, and it was actually the other
way around.  X_density was originally designated to be the neutral density
of element X, and sometime later X_p0 was added as an alias of this.  I'll
look to see if I can find the exact references for when this happened.


On Fri, Mar 3, 2017 at 2:01 PM, Nathan Goldbaum <nathan12343 at gmail.com>

> Hi Lauren,
> Thanks for the detailed report. It was very straightforward to reproduce
> what you're seeing using one of the test cosmological datasets on
> yt-project.org/data.
> I'm pretty sure you've stumbled across a bug in the way species fields are
> set up for Enzo.
> Here's what's happening:
> In yt-2, the field "H_NumberDensity" corresponds to the number density of
> all hydrogen ion species (i.e. HI + HII number density).
> In yt-3, for some reason, ('gas', 'H_number_density') represents the
> number density of just HI ions. To get what you had before, you'd need to
> defined a new field which sums ('gas', 'H_number_density') and ('gas',
> 'H_p1_number_density').
> The following IPython session illustrates the issue:
> In [10]: ds.fields.gas.H_density
> Out[10]: Alias Field for "('enzo', 'HI_Density')" (gas, H_density):
> (units: g/cm**3)
> In [11]: ds.fields.gas.H_p0_density
> Out[11]: Alias Field for "('gas', 'H_density')" (gas, H_p0_density):
> (units: g/cm**3)
> In [12]: ds.fields.gas.H_p1_density
> Out[12]: Alias Field for "('enzo', 'HII_Density')" (gas, H_p1_density):
> (units: g/cm**3)
> Right now ('gas', 'H_density') is an alias to ('enzo', 'HI_Density'), and
> ('gas', 'H_p0_density') is an alias to ('gas', 'H_density'). I'm pretty
> sure that's wrong, ('gas', 'H_p0_density') should be an alias to ('enzo',
> 'HI_Density') and ('gas', 'H_density') should be a derived field formed by
> summing HI_density and HII_density.
> Now, I'm pretty sure this is a bug, but I also don't normally with with
> Enzo multispecies data, so I'd like some confirmation about this from
> others who are more experienced with cosmological enzo data before I make a
> pull request.
> -Nathan
> On Fri, Mar 3, 2017 at 2:44 PM, Lauren Corlies <laurennc009 at gmail.com>
> wrote:
>> Hello,
>> I've been a yt user for a while now but have recently noticed something
>> concerning. A few months ago, I made the switch to yt3 and am currently
>> using the new yt 3.3.4
>> I've been working with recently generated, cosmological zoom in
>> simulations and I've generated a basic yt ray object.  When I plot the
>> hydrogen number density along the ray, the values that it's generating are
>> un-physically low (seen here <http://i.imgur.com/1C1oAVr.png>).
>> It's especially concerning because when I use the old yt2 installation:
>> Version = 2.7-dev
>> Changeset = 1f9ca06815d0
>> and generate a yt ray object with the exact same trajectory, the hydrogen
>> number density values are much more sensible (seen here
>> <http://i.imgur.com/tcDcNd8.png>). The rays in both yt versions have
>> mostly the same shape but there are some strong features in the yt2 version
>> than in the yt3 one.
>> The discrepancy is specifically with this field and not other intrinsic
>> fields like temperature or regular density (also attached).
>> Am I accessing the field incorrectly and there's a better way to get
>> these values with the new version of yt? Or is there something deeper
>> happening? The hydrogen number density is particularly important for the
>> ion densities and emission that I've been interested in.
>> All of the plots and the script <http://paste.yt-project.org/show/7066/>
>> to generate them are attached and posted online as described on the docs
>> page, tagged with my last name with links included as an attachment.
>> Thanks for the help,
>> Lauren Corlies
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