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

[Nathan Goldbaum]

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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>
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