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

Fri Mar 3 14:23:01 PST 2017

I'll take the blame for that naming convention.  I think my thought process
was that "nuclei" replaces "number" conceptually.

On Fri, Mar 3, 2017 at 2:16 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

>
>
> On Fri, Mar 3, 2017 at 4:10 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>> Ah, I see, this is covered in YTEP-0003:
>>
>> http://ytep.readthedocs.io/en/latest/YTEPs/YTEP-0003.html#mo
>> lecular-and-atomic-species-names
>>
>> And what Lauren wants to use in yt-3 is the "H_nuclei_number_density"
>> field. Except now that I check, we don't have that field at all, we only
>> have 'H_nuclei_density'. I'll submit a pull request that adds the number
>> density field automatically, but for now Lauren is going to need to define
>> her own nuclei number density field.
>>
>
> And it looks like ('gas', 'H_nuclei_density') *is* a number density after
> all:
>
> In [3]: ds.fields.gas.H_nuclei_density
> Out[3]: Derived Field (gas, H_nuclei_density): (units: cm**(-3))
>
> This is a tad annoying because the naming scheme here is inconsistent with
> the naming scheme of the other species fields.
>
> So that's the field you want to use Lauren. Hope my flailing around here
> over the course of this thread wasn't too confusing :)
>
>
>> Apologies for the noise about bugs!
>>
>> -Nathan
>>
>> On Fri, Mar 3, 2017 at 4:06 PM, Britton Smith <brittonsmith at gmail.com>
>> wrote:
>>
>>> 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.
>>>
>>> britton
>>>
>>> On Fri, Mar 3, 2017 at 2:01 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>>> wrote:
>>>
>>>> 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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